Amoeba now support front-loading evolution

 

I told you tyrosine kinases were old. It has now been discovered in amoeba, along with machinery to help front load the emergence of the immune system:

From Clarke M et al., Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.  Genome Biol. 2013 Feb 1;14(2):R11

BACKGROUND: The Amoebozoa constitute one of the primary divisions of eukaryotes encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.

RESULTS:

Ac encodes 15,455 compact intron rich genes a significant number of which are predicted to have arisen through interkingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors many with predicted orthologous functions in the innate immune systems of higher organisms.

CONCLUSIONS:

Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.

Remind me again why I am supposed to be wrong about the hypothesis of front-loading evolution?

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6 responses to “Amoeba now support front-loading evolution

  1. This is silly. Your statement, “I told you tyrosine kinases were old”, cannot be taken seriously, because evolutionists predicted tyrosine kinases were old. Indeed, evolutionists predict that most protein-signalling mechanisms evolved when our ancestors had very large population sizes, e.g. when they were once-celled, which permits more rapid exploration of sequence space for proteins. Complicated protein-signalling mechanisms or highly specific enzymatic functions must be old, but beneficial when they first appeared– this is a prediction of evolutionary theory, and it’s played out so far. Ed Marcotte at UT Austin has published a lot on deep homology.

    You are trying to pub-jack someone else’s research. If this (and many other things) were really predictions of Intellligent Design, why is it ID scientists never do the research themselves? Never. Ever.

    Creationists say there are hundreds– or thousands– or tens of thousands of scientists who believe in creationism and not evolution! Really!?

    Creationists are either many or they are few. If ID creationist scientists are many, why do THEY never do research like this? NEVER. EVER. If they are few, why do scientists find this hypothesis utterly absurd?

    Complicated protein-signalling mechanisms were beneficial when they first appeared. Thus, no front-loading. If you really want to prove front-loading, you have to prove a structure appeared when life was created supernaturally by God, but it was not functional at that time, and only required an environmental signal later, not random mutation and natural selection, to become functional.

    The fore-limbs on quadrupeds were later co-opted to make wings for birds and flippers for whales, dolphins, and penguins. Are the front legs on a salamander or dimetrodon also “proof of front-loading”? The fore-limbs on quadrupeds themselves were originally pectoral fins on lobe-finned fish. Are the fins on fish also “proof of front-loading”? What the hell ISN’T?

    You define “front-loading” so broadly that if it predicts anything at all, it appears to predict what evolution predicts. That’s fraudiction, not prediction.

    The fact that a signalling system appeared millions of years ago, and that highly modified duplicates of it took on a new function later, supports evolution by exaptation or co-opting of functions, as evolutionists have repeated many times.

  2. This is silly. Your statement, “I told you tyrosine kinases were old”, cannot be taken seriously, because evolutionists predicted tyrosine kinases were old.

    Can you please cite where someone used evolutionary theory to predict that tyrosine kinases would predate the appearance of metazoans?

    When tyrosine kinases were first identified in chaonoflagellates, it was not received as a confirmed prediction. It was a surprise:

    Next, she and her colleagues surveyed the organism’s genes at a high level and quickly discovered that it contains genes that were previously thought to only exist in animals. The big surprise was that two of those genes are actually used by animals to express proteins for cell adhesion and cell communication. In other words, a single-celled animal is making proteins that are seemingly essential only to multicellular animals.

    “It’s amazing.” King says. “We interpret that as evidence that some of the protein machinery for multicellularity actually evolved before the origin of animals, before multicellularity itself. The proteins predated their current function in animals.”
    [….]
    “I was surprised to learn that so much of animal biology was in place before the origin of animals,” King says. “And I think that’s what motivates most scientists–not learning that you were right, but learning that you were wrong.”

    Indeed, evolutionists predict that most protein-signalling mechanisms evolved when our ancestors had very large population sizes, e.g. when they were once-celled, which permits more rapid exploration of sequence space for proteins.

    We are not talking about “protein-signaling mechanisms.” We are talking about a specific example of such a mechanism – an example that was “previously thought to only exist in animals.”

    You are trying to pub-jack someone else’s research.

    No, all I am doing is showing how data about our world indicate that front-loading is plausible.

    If this (and many other things) were really predictions of Intellligent Design, why is it ID scientists never do the research themselves? Never. Ever.

    Probably because most of them are creationists and a anti-evolutionary perspective is not a solid foundation for a fruitful research program.

    You define “front-loading” so broadly that if it predicts anything at all, it appears to predict what evolution predicts. That’s fraudiction, not prediction.

    All you are telling me here is that you don’t understand my hypothesis of front-loading. My hypothesis begins with a simple question – would it be possible to design/guide evolution given the reality of random mutations and selection? Then, if so, HOW might one do this?

    This blog has dozens of essays that explore things from this angle.

  3. Your citation from this blog post (undated, but actually Dec. 15, 2010) just happened to insert a “creationist ellipsis”, and whenever I see creationists write “…” I have to check what’s in the “…” Immediately after “The proteins predated their current function in animals”, we read:

    According to King, this “a classic example of co-option,” an evolutionary process in which an existing biological structure or system is adapted for a new function.” [“Target Health Global”, Dec. 15, 2010]

    Wonder why you left that out. “Classic example” means as in textbook, what’s taught to every undergraduate. Is the source you cited, as an authority, still considered to be an authority by you? Or is it no longer an authority now that the full form undermines what you wrote?

    Let’s compare the source you cited, which you treated as an authority (at least in the form in which you edited it), against what I wrote:

    The fact that a signalling system appeared millions of years ago, and that highly modified duplicates of it took on a new function later, supports evolution by exaptation or co-opting of functions, as evolutionists have repeated many times.

    Strangely similar, hmm. I can’t entirely blame you for being fooled by the blog post you cited which does over-hype the “Gosh! I’m shocked!” nature of the results, which in fact are not very surprising. Such hyping of results is, alas, common in the muggle press. For the muggle press, every discovery is a Kuhnian “Paradigm Shift.”

    Now you ask a good question: “Can you please cite where someone used evolutionary theory to predict that tyrosine kinases would predate the appearance of metazoans?

    Fair enough. I go to Wikinome and look at their page for “Tyrosine Kinase evolution”, but not the current revision, let’s go waaaay back to the revision of 21 Aug 2009, pre-dating your blog source.

    “Tyrosine Kinases… [Their] overall sequences are most similar to the diverse TKL [Tyrosine-Kinase-Like] group, from which they may have emerged. The first clear TKs are seen in holozoans – the unicellular protists intermediate between fungi and animals – though possible TKs have also been seen in a few other basal lineages.” [Wikinome page for “Evolution of Tyrosine Kinases”, revision of 21 Aug 2009]

    So TK’s must predate metazoans, and the TKL group is found in most eukaryotic lineages, including notably plants. This page considers it likely that TK’s evolved from TKL enzymes (duh!). Continuing with this page, more detail on TKL’s:

    “TKL… This group is most similar to the TKs in sequence and structure, but is found in most eukaryotic lineages. In plants and Dictyostelium there is strong evidence that TKLs can act as tyrosine kinases. In both cases, the family is expanded, and many are found as transmembrane receptors, like most TKs are. In Dictyostelium, six TKLs have been shown to phosphorylate Tyr (Goldberg et al., 2006) and four others are fused to SH2 domains, suggesting that they do likewise.

    Homologs of metazoan GSK3, c-Cbl (no pTyr sites conserved!) and STAT proteins that are regulated by Tyr phosphorylation have conserved these phosphorylation sites in Dictyostelium (unpublished), and both STAT and GSK3 have been shown to be Tyr-phosphorylated by Dictyostelium TKL kinases, suggesting that these control mechanisms are ancient, and that the later invention of TKs may have displaced TKLs from this role and these specific substrates.

    In plants, several TKLs (IRAKs) have been implicated in tyrosine phosphorylation…

    It bears repeating: “suggesting that these control mechanisms are ancient.”

    The current revision of this page is better written and has more complete information.

    You state: “All you are telling me here is that you don’t understand my hypothesis of front-loading.”

    No, I understand your thesis perfectly well, it’s the cutting edge science of the twelfth century, the scholastics and their teleology: you observe how something acts, and then only after the fact you say, it’s purpose is to act the way it acts. The problem with that is that you can’t predict things ahead of time, because you can’t deduce the purpose of things by an independent method, independent of how they act, so you’re stuck with circular logic.

    My hypothesis begins with a simple question – would it be possible to design/guide evolution given the reality of random mutations and selection? Then, if so, HOW might one do this?

    No, that is not scientific. Instead of asking HOW an invisible spook might “guide” evolution, you should instead ask “How may I TEST my hypothesis via a double-blind test? And what is my negative control?”

    Again I repeat: the mechanisms you describe are functional when they first appear, they just do not have their modern function. If front-loading really made predictions DIFFERENT from evolutionary theory, then these mechanisms should be non-functional when they appear, and somehow protected from deleterious mutations (by some non-NS mechanism) for 500 million years or whatever. If OTOH front-loading just predicts that mechanisms are functional when they appear, and change function later, then it IS evolutionary theory.

  4. Your citation from this blog post (undated, but actually Dec. 15, 2010) just happened to insert a “creationist ellipsis”, and whenever I see creationists write “…” I have to check what’s in the “…”

    Error #1: That is not a quote from that blog. That is a quote from ScienceMatters@Berkeley: College of Letters & Science; University of California, Berkeley; Vol2, Issue 17, Dec 2005/Jan 2006. Here is the original link (no longer functional): http://sciencematters.berkeley.edu/archives/volume2/issue17/story1.php

    Error#2: I am not a creationist. That you think I am means your thinking is clouded by stereotypes. And this will lead you to make all sorts of errors. For example:

    Immediately after “The proteins predated their current function in animals”, we read:
    “According to King, this “a classic example of co-option,” an evolutionary process in which an existing biological structure or system is adapted for a new function.” [“Target Health Global”, Dec. 15, 2010]
    Wonder why you left that out. “Classic example” means as in textbook, what’s taught to every undergraduate.

    Error #3: Of course this is a classic example of co-option. Nowhere did I say or imply that it was not. Co-option is something we would expect from front-loading, as I explained years ago. One example: http://designmatrix.wordpress.com/2010/11/04/front-loading-and-preadaptations/

    So why did I leave that out? Despite what your stereotypes insist, it was not some sneaky, creationist trick. I left it out for the same reason I left this out: “As one of only a handful of laboratories around the world studying the choanoflagellates using methods from molecular and cell biology, King’s research group is developing most of their techniques from scratch. Meanwhile, they’re collaborating with scientists from the Department of Energy’s Joint Genome Institute, who are sequencing the whole genome of a choanaoflagellate.”

    I left those parts out because neither point is relevant to the point we are discussing. We are not talking about co-option, or whether King’s lab is one of the few to study choanoflagellates. I accept both. The point of contention is you insisting that evolutionary theory predicted that tyrosine kinases would long predate the appearance of metazoa. The quotes I cited show you to be wrong. Prior to King’s discovery, the scientific community thought tyrosine kinases were restricted to metazoans and King herself was surprised by the discovery.

    Is the source you cited, as an authority, still considered to be an authority by you? Or is it no longer an authority now that the full form undermines what you wrote?

    Clearly, you do not understand my position and argument, as there is nothing in that article that undermines my position. Nothing.

    Let’s compare the source you cited, which you treated as an authority (at least in the form in which you edited it), against what I wrote:

    “The fact that a signalling system appeared millions of years ago, and that highly modified duplicates of it took on a new function later, supports evolution by exaptation or co-opting of functions, as evolutionists have repeated many times.”

    Strangely similar, hmm.

    I have been talking about co-option from the teleological perspective for about 10 years now.

    I can’t entirely blame you for being fooled by the blog post you cited which does over-hype the “Gosh! I’m shocked!” nature of the results, which in fact are not very surprising. Such hyping of results is, alas, common in the muggle press. For the muggle press, every discovery is a Kuhnian “Paradigm Shift.”

    The only thing that has happened here is that you have fooled yourself by your own reliance on stereotype and hasty conclusions. And there is no need for you to smear ScienceMatters@Berkeley.
    The points that I quoted have nothing to do with any “muggle press.” When the writer notes that tyrosine kinases were previously thought to only exist in animals, that is simply a part of the history of science. And it’s not just the “muggle press” who noted the discovery as a surprise – you can see from the quote of King herself, she was surprised.

    Now you ask a good question: “Can you please cite where someone used evolutionary theory to predict that tyrosine kinases would predate the appearance of metazoans?”

    Fair enough. I go to Wikinome and look at their page for “Tyrosine Kinase evolution”, but not the current revision, let’s go waaaay back to the revision of 21 Aug 2009, pre-dating your blog source.

    This is just too much. What you “found” was three years older than ScienceMatters@Berkeley article and six years after King published the Choanoflagellate genome. So of course it will summarize what was already known! So what you found was irrelevant. You need to find a scientific paper from the 1990s where someone uses evolutionary theory to predict that tyrosine kinases should be much, much older than metazoans.

    Look, you insisted, in a matter of fact manner, “This is silly. Your statement, “I told you tyrosine kinases were old”, cannot be taken seriously, because evolutionists predicted tyrosine kinases were old.” The fact that you are now try to support your claim by citing something that was written six years after King made it clear TRK’s were not metazoan specific tells us your bold, sneering claim was something you pulled out of your ass.

    It bears repeating: “suggesting that these control mechanisms are ancient.”

    Of course. Is that somehow supposed to indicate front-loading is false? Look, if these control mechanisms are ancient, would that make it easier or harder for metazoans to emerge?

    No, I understand your thesis perfectly well,

    Hogwash. If you did, you would not think evolution by co-option was something that undermined my position.

    it’s the cutting edge science of the twelfth century, the scholastics and their teleology: you observe how something acts, and then only after the fact you say, it’s purpose is to act the way it acts.

    Since you come to the table with such preconceptions, it is no wonder you cannot understand my position.

    The problem with that is that you can’t predict things ahead of time, because you can’t deduce the purpose of things by an independent method, independent of how they act, so you’re stuck with circular logic.

    http://designmatrix.wordpress.com/2009/01/18/four-expectations-from-front-loading/

    Me: My hypothesis begins with a simple question – would it be possible to design/guide evolution given the reality of random mutations and selection? Then, if so, HOW might one do this?

    You: No, that is not scientific.

    Who cares? I never said my case was scientific, as there is no reason to think science could ever process these types of questions. Yet the questions remain. If you are unwilling to ask them, and unwilling to think about them, you will remain enslaved to your stereotypes when trying to understand my views (then again, I suspect you have no interest in trying to understand my views).

    Instead of asking HOW an invisible spook might “guide” evolution, you should instead ask “How may I TEST my hypothesis via a double-blind test? And what is my negative control?”

    How silly. This topic is far too ambiguous to be run like some drug test.

    Again I repeat: the mechanisms you describe are functional when they first appear, they just do not have their modern function.

    No one said otherwise. They were simply preadapted to reach their modern function.

    If front-loading really made predictions DIFFERENT from evolutionary theory, then these mechanisms should be non-functional when they appear, and somehow protected from deleterious mutations (by some non-NS mechanism) for 500 million years or whatever.

    This too is silly. Why would a designer design something to be non-functional for 500 million years and then add on some contraption that somehow protects it from change for 500 million years? The objective of front-loading would not be to come up with something that would compel Diogenes to infer design billions of years later. They objective would be to come up with ways to guide evolution given that it is a process saturated with random mutations and selection.

    If OTOH front-loading just predicts that mechanisms are functional when they appear, and change function later, then it IS evolutionary theory.

    It’s also a very clever design strategy.

  5. Diogenes,
    It’s been almost two weeks. Aren’t you going to reply?

  6. For the record – Diogenes never replied.

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