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New genes required for the Cambrian explosion

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  • New genes required for the Cambrian explosion

    157 new genes, in fact, just for the origin of bilaterians.

    Source: Evolution News

    ... the article hints a key point that we’ve made repeatedly here — that global changes such as increased ocean oxygenation or other ecological factors are not sufficient to explain the origin of new genetic information needed in the Cambrian explosion...

    Source

    © Copyright Original Source


    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  • #2
    Originally posted by lee_merrill View Post
    157 new genes, in fact, just for the origin of bilaterians.

    Source: Evolution News

    ... the article hints a key point that we’ve made repeatedly here — that global changes such as increased ocean oxygenation or other ecological factors are not sufficient to explain the origin of new genetic information needed in the Cambrian explosion...

    Source

    © Copyright Original Source


    Blessings,
    Lee
    The Cambrian "explosion" took between 20-30 million years. That's plenty of time for whole gene families to have evolved. You need to quit parroting the scientific ignorance you get from Creationists like AIG and the DI.

    Comment


    • #3
      Originally posted by lee_merrill View Post
      157 new genes, in fact, just for the origin of bilaterians.

      Source: Evolution News

      ... the article hints a key point that we’ve made repeatedly here — that global changes such as increased ocean oxygenation or other ecological factors are not sufficient to explain the origin of new genetic information needed in the Cambrian explosion...

      Source

      © Copyright Original Source


      Blessings,
      Lee
      Conclusion requires an anti-science agenda, and 'arguing from ignorance' speculation.
      Glendower: I can call spirits from the vasty deep.
      Hotspur: Why, so can I, or so can any man;
      But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

      go with the flow the river knows . . .

      Frank

      I do not know, therefore everything is in pencil.

      Comment


      • #4
        Originally posted by HMS_Beagle View Post

        The Cambrian "explosion" took between 20-30 million years. That's plenty of time for whole gene families to have evolved. You need to quit parroting the scientific ignorance you get from Creationists like AIG and the DI.
        As the renown geologist Donald R. Prothero has noted, the Cambrian "Explosion" is far better viewed as a slow fuse taking tens of millions of years.

        From his Evolution: What the Fossils Say and Why it Matters[1]:

        The problem with the creationist' fascination with the Cambrian explosion is that it's all wrong! The major groups of invertebrate fossils do not all appear suddenly at the base of the Cambrian but are spaced out over strata spanning 80 million years -- hardly an instantaneous "explosion"! Some groups appear tens of millions of years earlier than others. And preceding the "Cambrian explosion" was a long slow buildup to the first appearance of typical Cambrian shelled invertebrates.


        Or if you prefer something from a more Christian perspective. From BioLogos, established by the geneticist Francis Collins (who led the Human Genome Project and is the director of the National Institutes of Health and author of The Language of God: A Scientist Presents Evidence for Belief):

        Source: The Cambrian “Explosion”, Transitional Forms, and the Tree of Life


        Defining the Cambrian “explosion” is not as straightforward as it might seem. Although there was clearly a major burst of evolutionary innovation and diversification in the first 20 million years or so of the Cambrian, this was preceded by an extended period of about 40 million years during which metazoans (multicellular animals) arose and attained critical levels of anatomical complexity.



        Source

        © Copyright Original Source




        There are two things worth noting.

        First, while most of the phyla that are around today arose during the Cambrian (some like sponges, annelids and cnidarians arose earlier in the Precambrian[2]) they are not anything like what we see today. Back in the Cambrian there were no amphibians, reptiles, birds, or mammals (much less humans). Simply put there were hardly any chordates at all, to say nothing of vertebrates. As far as fish go, they were limited to primitive, invertebrate jawless creatures that one can classify as "fish" like Haikouichthys, but no fully developed modern fish. Fish like we commonly find today are nowhere to be found in Cambrian deposits.

        And there were few if any terrestrial insects (which represent well over 50% of all animal life currently existing on the planet).

        Flora-wise there were not only any flowering plants (angiosperms) there weren't even any gymnosperms from which they arose from. There wasn't much in the way of terrestrial plants at all (vascular plants first arose during the Silurian long after end of the Cambrian).

        As Graham Budd and Sören Jensen noted in their 2000 paper, A critical reappraisal of the fossil record of the bilaterian phyla, Cambrian life was still unlike almost anything that we observe today. While a number of phyla appear to have diverged in the Early Cambrian or earlier, most of the phylum-level body plans first appear in the fossil record much later on.

        This flies in the face of the oft repeated claim made by creationists that, as Jonathan Wells (Senior Fellow at the Discovery Institute) puts it, "Most animal forms appear in the form they currently have in the present." Nope. Not even remotely close.

        Second, the so-called Cambrian Explosion is hardly a unique event. There have been actually been several rapid diversifications of life during earth's history including at least one 30 million years before to the Cambrian "Explosion" (the "Avalon explosion" of the Ediacaran biota in the Precambrian). The Cambrian "Explosion" is just one more meaning that there really is nothing unique about adaptive radiations like that.

        Also there was the Ordovician radiation or biodiversity event (considered one of the most extensive diversifications of life seen), which saw the diversification of trilobites, echinoderms and brachiopods, as well as the rise of true corals, among other things.

        There was a Devonian radiation, which saw another re-radiation of trilobite species, as well as the rise and diversification of large predatory fish such as sharks, ray-finned fish, lobe-finned fish, placoderms, and acanthodians.

        The Devonian also experienced a one-time explosion in the evolution of terrestrial plants: after a cryptic history beginning about 450 mya, land plants underwent a uniquely rapid adaptive radiation. And speaking of terrestrial plants 100 mya (mid Cretaceous) witnessed a rapid radiation of angiosperms (flowering plants) as they diversified.

        At the end of the Permian, when an estimated 90% of species and 50-60% of families appear to have become extinct and were replaced by a small number of genera which rapidly diversified to fill a wide number of ecological niches during the early Triassic. For instance Lystrosaurus, a small dicynodont therapsid, were by far the most common terrestrial vertebrates for millions of years and appear to have accounted for roughly 90% or more of early Triassic terrestrial vertebrates.

        And the most recent was the Cenozoic radiation of mammals after the Cretaceous. So the Cambrian "Explosion" is just one more meaning that there really is nothing unique about adaptive radiations like that.


        As a final note, saying that "increased ocean oxygenation ... are not sufficient to explain the origin of new genetic information needed in the Cambrian explosion" is lubricous in the extreme. The Great Oxidation Event ended 1.5 Billion years before the start of the Cambrian. That is more than three times as much time as there is between the end of the Cambrian (roughly 485.4 million years ago) and now and look at how much things have changed since then.








        1. While published almost 14 years ago, I still highly recommend it for anyone interested in the topic

        2. And at least one phyla arose after the Cambrian. Bryozoa, for instance, is not known before the early Ordovician.

        I'm always still in trouble again

        "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
        "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
        "Of course, human life begins at fertilization that’s not the argument." --Tassman

        Comment


        • #5
          Well, 25 million years / 157 genes is on average, about 160,000 years to create and fix each gene. Now I realize that evolution proceeds in parallel, so this is an average, yet this is indeed explosive, and just for some genes for bilaterians!

          Blessings,
          Lee
          "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

          Comment


          • #6
            Originally posted by lee_merrill View Post
            Well, 25 million years / 157 genes is on average, about 160,000 years to create and fix each gene. Now I realize that evolution proceeds in parallel, so this is an average, yet this is indeed explosive, and just for some genes for bilaterians!

            Blessings,
            Lee
            No it is not an average. You even acknowledged the 157 genes evolved in parallel over that time. If it takes 6 days for a convoy of 12 ships to cross the Atlantic ocean that doesn't mean each ship took an average of a half day to cross.

            Comment


            • #7
              Originally posted by lee_merrill View Post
              Well, 25 million years / 157 genes is on average, about 160,000 years to create and fix each gene. Now I realize that evolution proceeds in parallel, so this is an average, yet this is indeed explosive, and just for some genes for bilaterians!

              Blessings,
              Lee
              You keep ignoring that these genes are not evolving in a sequence with them going one at a time as if in a queue. And I know that you've been informed of this on several occasions.

              I'm always still in trouble again

              "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
              "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
              "Of course, human life begins at fertilization that’s not the argument." --Tassman

              Comment


              • #8
                Originally posted by rogue06 View Post
                You keep ignoring that these genes are not evolving in a sequence with them going one at a time as if in a queue. And I know that you've been informed of this on several occasions.
                I question how many truly 'new' genes there were through this period. All the basic forms and morphologies existed before the Cambrian explosion.
                Glendower: I can call spirits from the vasty deep.
                Hotspur: Why, so can I, or so can any man;
                But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

                go with the flow the river knows . . .

                Frank

                I do not know, therefore everything is in pencil.

                Comment


                • #9
                  Originally posted by HMS_Beagle View Post

                  No it is not an average. You even acknowledged the 157 genes evolved in parallel over that time. If it takes 6 days for a convoy of 12 ships to cross the Atlantic ocean that doesn't mean each ship took an average of a half day to cross.
                  Good point! Though I don't expect 157 genes are going to arrive all at once at the end of 25 million years, either.

                  Blessings,
                  Lee
                  "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

                  Comment


                  • #10
                    Originally posted by lee_merrill View Post
                    Good point! Though I don't expect 157 genes are going to arrive all at once at the end of 25 million years, either.

                    Blessings,
                    Lee
                    Genes do not arrive, science does not believe in the 'Stork.' .Please reread rogue06 posts and respond intelligently.
                    Glendower: I can call spirits from the vasty deep.
                    Hotspur: Why, so can I, or so can any man;
                    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

                    go with the flow the river knows . . .

                    Frank

                    I do not know, therefore everything is in pencil.

                    Comment


                    • #11
                      Originally posted by lee_merrill View Post
                      157 new genes, in fact, just for the origin of bilaterians.

                      [cite=Evolution News]... the article hints a key point that we’ve made repeatedly here — that global changes such as increased ocean oxygenation or other ecological factors are not sufficient to explain the origin of new genetic information needed in the Cambrian explosion...
                      You know, before you go dumping quotes like that on us, it's probably worth asking a simple question: why not? What evidence do they actually present that these factors aren't sufficient.

                      I've read it, and i'll save you the time: they present none.

                      In any case, the whole post was obviously written by someone who doesn't bother looking into the underlying biology of the paper, and is just trying to score rhetorical points. For one, it's citing something in the paper that's clearly wrong about the origin of bilaterians: we now have obvious fossil evidence that they predated the Cambrian. So, the time frame for their evolution isn't the length of the Cambrian, but some indeterminate length of time in the Ediacaran and possibly prior to that. Why a recent paper gets that wrong, i'm not sure, but i assume it's a matter of timing (the fossil was published while this work would have been in progress) and the fact that these are molecular guys, and probably aren't that up on fossils.

                      Moving on...

                      The person who wrote the blog post doesn't understand what "new" genes involves. For starters, he quotes a bit about the nodal pathway, which determines the left/right axis. Paper says that the pathway had to be evolved in the metazoan lineage, which is true. But some of its components exist in choanoflagellates, the closest relatives to metazoans. So, while the pathway doesn't function in those organisms, at least some of its parts were present.

                      Zinc finger transcription factors are widespread in life, including in prokaryotes and archaea. There may be new versions of these genes in metazoans, but they are almost certainly evolved duplicates of existing zinc finger genes.

                      If you look at the choanoflagellate genome, you'll also find parts of metazoan genes hooked up in odd combinations. Most complex proteins are an array of functional units called "domains". So you may have a kinase domain, protein interaction domain, and cross-membrane domain, etc. A number of choanoflagellate genes have things like the protein interaction domain of one metazoan gene in the same protein as the kinase domain of a different one. So, a lot of the "new" genes in metazoans are simply the result of swapping domains from existing genes around.

                      So, to the extent that there's any argument whatsoever in the blog post, it's "OMG, look at how many new genes there are!" When in reality, we have a vast, indeterminate span of many tens of millions of years, fewer new ones than it sounds like, and known mechanisms for forming them. Once again, the Discovery guys a bunch of clowns and you should stop paying any attention to them whatsoever.

                      Given how many times they've said obviously moronic things, why do you keep reading them?
                      "Any sufficiently advanced stupidity is indistinguishable from trolling."

                      Comment


                      • #12
                        Originally posted by TheLurch View Post
                        What evidence do they actually present that these factors aren't sufficient.
                        I think this was meant:

                        Source: eLife

                        While deep-ocean oxygenation (Canfield et al., 2007), the availability of calcium (Jackson et al., 2010), or ecological interactions (Budd and Jensen, 2017) likely played a role, genetic changes in the bilaterian ancestor must ultimately have constituted its molecular basis.

                        © Copyright Original Source



                        we now have obvious fossil evidence that they predated the Cambrian.
                        Reference, please?

                        But some of its components exist in choanoflagellates, the closest relatives to metazoans. So, while the pathway doesn't function in those organisms, at least some of its parts were present.
                        That's fine, and I'm sure the blog writer doesn't insist that all genes come about de novo.

                        However, in the referenced article, we read:

                        Source: eLife

                        The other four domains were restricted to bilaterians, like the proteins they belong to (Supplementary file 1–Supplementary Table 9), a finding compatible with the de novo birth of these five genes. Similarly, sequences without known protein domains were also detectable in arthropod- and vertebrate-specific orthogroups (Figure 2) and, more generally, in approximately 40% of the 69,114 orthogroups with more than ten species. These findings open the possibility that, across opisthokonts, many lineage-specific genes are uncharacterised and may contain previously undescribed protein domains and novel lineage-specific domains, emphasising the involvement of gene birth in lineage evolution on a broad scale.

                        © Copyright Original Source



                        Zinc finger transcription factors are widespread in life, including in prokaryotes and archaea. There may be new versions of these genes in metazoans, but they are almost certainly evolved duplicates of existing zinc finger genes.
                        Source: eLife

                        Indeed, we identified in the 157 bilaterian-specific orthogroups two relevant zinc finger transcription factors.

                        © Copyright Original Source


                        So 2 out of 157, not a major contribution here.

                        So, a lot of the "new" genes in metazoans are simply the result of swapping domains from existing genes around.
                        Reference, please?

                        Source: eLife

                        revealing that bilaterian-specific genes form a dense network in which about 50% of the factors (83 distinct factors) are connected to one another (Figure 8A). These interactions form several subnetworks involved in regulating key aspects of bilaterian development, such as chromatin organisation and transcriptional regulation (subnetwork A), myogenesis (subnetwork B), mesoderm formation and left-right asymmetry (the Nodal pathway, subnetwork C: see also Figure 8B), neurogenesis (subnetwork D), and physiology (subnetwork E).

                        © Copyright Original Source


                        So about half seem to form a regulatory network, which increases the complexity enormously. This is not just 157 new genes.

                        Blessings,
                        Lee
                        "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

                        Comment


                        • #13
                          Originally posted by lee_merrill View Post
                          I think this was meant:

                          Source: eLife

                          While deep-ocean oxygenation (Canfield et al., 2007), the availability of calcium (Jackson et al., 2010), or ecological interactions (Budd and Jensen, 2017) likely played a role, genetic changes in the bilaterian ancestor must ultimately have constituted its molecular basis.

                          © Copyright Original Source




                          Reference, please?


                          That's fine, and I'm sure the blog writer doesn't insist that all genes come about de novo.

                          However, in the referenced article, we read:

                          Source: eLife

                          The other four domains were restricted to bilaterians, like the proteins they belong to (Supplementary file 1–Supplementary Table 9), a finding compatible with the de novo birth of these five genes. Similarly, sequences without known protein domains were also detectable in arthropod- and vertebrate-specific orthogroups (Figure 2) and, more generally, in approximately 40% of the 69,114 orthogroups with more than ten species. These findings open the possibility that, across opisthokonts, many lineage-specific genes are uncharacterised and may contain previously undescribed protein domains and novel lineage-specific domains, emphasising the involvement of gene birth in lineage evolution on a broad scale.

                          © Copyright Original Source




                          Source: eLife

                          Indeed, we identified in the 157 bilaterian-specific orthogroups two relevant zinc finger transcription factors.

                          © Copyright Original Source


                          So 2 out of 157, not a major contribution here.


                          Reference, please?

                          Source: eLife

                          revealing that bilaterian-specific genes form a dense network in which about 50% of the factors (83 distinct factors) are connected to one another (Figure 8A). These interactions form several subnetworks involved in regulating key aspects of bilaterian development, such as chromatin organisation and transcriptional regulation (subnetwork A), myogenesis (subnetwork B), mesoderm formation and left-right asymmetry (the Nodal pathway, subnetwork C: see also Figure 8B), neurogenesis (subnetwork D), and physiology (subnetwork E).

                          © Copyright Original Source


                          So about half seem to form a regulatory network, which increases the complexity enormously. This is not just 157 new genes.

                          Blessings,
                          Lee
                          Terrible selective sound bite citation out of context of sources(?). The diversification in the 40 million years before the Cambrian explosion is well documented. The Lurch will address your continued foolishness as before, as in the long history of your threads and posts.
                          Glendower: I can call spirits from the vasty deep.
                          Hotspur: Why, so can I, or so can any man;
                          But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

                          go with the flow the river knows . . .

                          Frank

                          I do not know, therefore everything is in pencil.

                          Comment


                          • #14
                            Originally posted by TheLurch View Post
                            You know, before you go dumping quotes like that on us, it's probably worth asking a simple question: why not? What evidence do they actually present that these factors aren't sufficient.

                            I've read it, and i'll save you the time: they present none.

                            In any case, the whole post was obviously written by someone who doesn't bother looking into the underlying biology of the paper, and is just trying to score rhetorical points. For one, it's citing something in the paper that's clearly wrong about the origin of bilaterians: we now have obvious fossil evidence that they predated the Cambrian.
                            And it isn't something that took place during the last year or so, so not being aware of that cannot be excused on those grounds

                            From 2012: Bilaterian Burrows and Grazing Behavior at >585 Million Years Ago

                            From 2008: Precambrian trace fossils and the rise of bilaterian animals

                            Also 2008: The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

                            From 2003: Early Evolution of the Bilateria

                            From 2000: Age of Neoproterozoic Bilatarian Body and Trace Fossils, White Sea, Russia: Implications for Metazoan Evolution

                            From 1997: The Late Precambrian fossil Kimberella is a mollusc-like bilaterian organism

                            From 1994: Late Precambrian bilaterians: grades and clades


                            And Spriggina, which were discovered way back in the late 1950s clearly displays a bilateral body plan and Kimberella, discovered in 1964, is usually considered the earliest bilateral (555 to 558 myo -- which would predate confirmed Spriggina fossils by 5 to 8 million years and the beginning of the Cambrian by 14 to 17 million years), although Vernanimalcula is considerably older (600 to 580 million years ago), it's classification as a bilateral is controversial.

                            Last edited by rogue06; 11-16-2020, 07:21 AM.

                            I'm always still in trouble again

                            "You're by far the worst poster on TWeb" and "TWeb's biggest liar" --starlight (the guy who says Stalin was a right-winger)
                            "Overall I would rate the withdrawal from Afghanistan as by far the best thing Biden's done" --Starlight
                            "Of course, human life begins at fertilization that’s not the argument." --Tassman

                            Comment


                            • #15
                              Originally posted by lee_merrill View Post
                              I think this was meant:

                              Source: eLife

                              While deep-ocean oxygenation (Canfield et al., 2007), the availability of calcium (Jackson et al., 2010), or ecological interactions (Budd and Jensen, 2017) likely played a role, genetic changes in the bilaterian ancestor must ultimately have constituted its molecular basis.

                              © Copyright Original Source

                              But that doesn't provide any evidence at all. All this quote says is that genetic changes must have happened (which, duh, that's what evolution is). It doesn't say that those changes couldn't have been in response to environmental changes. So, my point stands: they made a claim and provided absolutely zero evidence to back it up.

                              Why do you like garbage like that so much? Is it because you don't understand what evidence looks like?


                              Originally posted by lee_merrill View Post
                              Reference, please?
                              https://www.nature.com/articles/s41586-019-1522-7

                              Originally posted by lee_merrill View Post
                              That's fine, and I'm sure the blog writer doesn't insist that all genes come about de novo.
                              But it's not fine. As far as i can infer what the author is positing through his poorly written text, he's basically claiming that evolving an entirely new pathway is wildly improbable. But if parts of the pathway aren't entirely new, then that claim is completely bogus.



                              Originally posted by lee_merrill View Post
                              However, in the referenced article, we read:

                              Source: eLife

                              The other four domains were restricted to bilaterians, like the proteins they belong to (Supplementary file 1–Supplementary Table 9), a finding compatible with the de novo birth of these five genes. Similarly, sequences without known protein domains were also detectable in arthropod- and vertebrate-specific orthogroups (Figure 2) and, more generally, in approximately 40% of the 69,114 orthogroups with more than ten species. These findings open the possibility that, across opisthokonts, many lineage-specific genes are uncharacterised and may contain previously undescribed protein domains and novel lineage-specific domains, emphasising the involvement of gene birth in lineage evolution on a broad scale.

                              © Copyright Original Source

                              Nobody's arguing that new genes don't evolve. They do all the time. The issue is what we can infer from that fact.

                              Originally posted by lee_merrill View Post
                              Source: eLife

                              Indeed, we identified in the 157 bilaterian-specific orthogroups two relevant zinc finger transcription factors.

                              © Copyright Original Source


                              So 2 out of 157, not a major contribution here.
                              Yes, but the fact that neither you nor the author knew about those two is rather telling, don't you think? How many other "new" genes in this report might be similar, but you wouldn't be able to recognize it?

                              It should at least give you some pause and cause you to re-evaluate your opinion on this one.

                              Originally posted by lee_merrill View Post
                              Reference, please?
                              https://www.nature.com/articles/nature06617

                              Originally posted by lee_merrill View Post
                              So about half seem to form a regulatory network, which increases the complexity enormously. This is not just 157 new genes.
                              No, it's not. But you wouldn't expect that, would you? The difference between bilaterians and everything else is their development. So, you'd expect most of the genes distinct to bilaterians to be involved in regulating development, which means that they're going to be involved in overlapping processes, and thus are more likely to interact. And the reference i provided immediately above this shows that many of the domains that have been shifted into metazoan-specific combinations mediate protein interactions, this is also a likely outcome of the origin of the genes.

                              In other words, you have an obvious mechanism (domain swapping) for generating novel protein interactions, and an obvious selective pressure (operating in overlapping process) for retaining interaction domains. So this is exactly the outcome you'd expect.
                              "Any sufficiently advanced stupidity is indistinguishable from trolling."

                              Comment

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