11 ms·

The Very First Animal Appeared Amid an Explosion of DNA

98 points by montrose 8y ago

chiefalchemist 8y ago
"Humans and sharks, for example, make hemoglobin using nearly identical genes. That means hemoglobin genes were already present in their common ancestor." Um. If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? At two different times? At two different branches on the species tree? Not really my area but there seems to be an assumption that species development (dare I say evolution) was linear, with humans being the ultimate achievement in that process. But doesn't the fact that genes mutate - sometimes triggered by viruses - imply the process was not at all linear?
- phito 8y ago
  Convergent evolution is totally a thing. What if at some point in time, there was a virus running around and copy pasting some dna around?
  - mannykannot 8y ago
    I think it is generally true to say that individual genes don't work in a vacuum, and neither do the biological mechanisms they encode for, so the transferred DNA would have to contain a suite of co-dependent genes. Admittedly, there is a counter-example in the transfer of genes conferring resistance to a particular pathogen. I think it is also true to say that convergent evolution often produces results that differ genetically, even though the resulting phenotypes serve the same purpose.
  - fifnir 8y ago
    Check out these guys: https://en.wikipedia.org/wiki/Transposable_element https://en.wikipedia.org/wiki/Transposable_element
  - stevenwoo 8y ago
    Like this retrotransposon? https://www.theatlantic.com/science/archive/2018/04/the-shellfish-gene/558131/ https://www.theatlantic.com/science/archive/2018/04/the-shel...
- shawabawa3 8y ago
  I'm not an expert in the field but my understanding is that DNA has a huge amount of "junk" in it. This junk doesn't do anything but can act as a fingerprint for where the DNA evolved from, as it's impossible for the junk to be evolved twice in exactly the same way
  - jbrooksuk 8y ago
    I'm sure the "junk" DNA does something, we just don't know what yet.
    - perl4ever 8y ago
      Seems to me, "junk DNA" could be "commented out" code, which provides resilience to selection pressure, but doesn't technically do anything right now.
      - ethelward 8y ago
        That's pseudogenes, but it's not a massive part of the non-coding DNA.
  - kingkawn 8y ago
    The concept of junk DNA was mostly taken apart a few years ago. Those sections often serve regulatory functions and other purposes related to controlling how genes are used and at what rates.
    - dekhn 8y ago
      You're referring to regulatory regions which really represent a tiny component of the genome (in terms of base fraction)... but nobody has really constructed a strong argument (that can be tested) that long stretches of Alu (which comprise most of the junk DNA) actually have a regulatory or other function. It's speculated those regions are gene foundries, but it's mostly speculation with limited evidence.
      - 8y ago
- gort 8y ago
  > Um. If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? At two different times? At two different branches on the species tree? Genes are long sequences of information. You could easily have quite different genes doing similar things, but if you have the very same gene (sans minor differences) it's just too unlikely to have originated completely independently twice. The closest thing I can imagine to your scenario is where, because of shared ancestry, 2 species have a certain gene, and then some minor mutation hits both of them, and now they both have some other gene. I suppose that's possible. But they already shared the original gene to start with.
  - lkrubner 8y ago
    If a mutation in a given gene leads to death 99.9999% of the time, but leads to oxygen transport the rest of the time, and the mutation happens many millions of times, then it is reasonable to think it could have been invented twice. Most of the time the mutation leads to death, but every once in a million times it leads to a happy result. Over the course of a few million years, the mutation happens many millions of times. In that scenario you would expect to happen at least twice, and probably much more often. As an example, write a simple program that randomly generates strings of letters from 1 to 20 characters in length. Then include an English dictionary in the program. Compare the randomly generated strings with the words in the dictionary. How often does the random process generate actual words? Not often, but sometimes, and that is all that is needed.
    - gort 8y ago
      Sure, but this is only possible if the original (shared) gene was really quite close to being able to transport oxygen.
    - rlpb 8y ago
      What if there are a million different possible genes that produce hemoglobin? In that case, if two different species were found to produce hemoglobin but use the same gene, then what would that imply? I think this is what grandparent meant by "You could easily have quite different genes doing similar things".
- zimpenfish 8y ago
  > there seems to be an assumption that species development (dare I say evolution) was linear, with humans being the ultimate achievement in that process Only amongst people who haven't done any reading or learning about evolution. > the process was not at all linear Indeed. > If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? Yes. But if the gene is nearly identical in sharks as in humans, the chance of that happening from convergent evolution would be small enough that "they have a common ancestor" is a much more likely cause.
  - kevin_thibedeau 8y ago
    There is always the possibility of horizontal gene transfer mediated by a pathogen.
    - glenneroo 8y ago
      Mosquitoes supposedly helped transfer bits of DNA between species, which over millions of years influenced multiple species... or is that because they were the pathogen carriers?
- huntertwo 8y ago
  Evolution is not linear. All species are at a different leaf of the tree of evolution from some sort of “proto-being” as the root node. Humans are no different than dogs or cacti. Humans may be the common ancestor of two different species that exist 1 million years in the future. It is definitely possible that the two same mutations for hemoglobin happened at different points in time, but as I understand it, there is an assumption of parsimony. In other words, it is much more likely that the creation of genes for hemoglobin for sharks and humans happened at the same time than at different times.
  - deleted 8y ago
    [deleted]
  - PurpleBoxDragon 8y ago
    >Humans are no different than dogs or cacti. I think we will always have a special place in the history books (perhaps not a pleasant one) because we were the first to have some ability to consciously edit not only our DNA but the DNA of other species. Thinking about it, if life begin in millions of different universes, there would seem to be one of two possible outcomes. Life eventually goes extinct (due to something happening on the planet that life can't evolve to survive, if nothing else the death of the planet's star), or life develops a species with enough intelligence to be able to modify their own evolution. An idea similar to the anthropic principal. Though different in that we are a sufficient end case for the anthropic principal, but we haven't reached a sufficient end case in regards to evolution (though we have begun to grasp it).
    - lostapathy 8y ago
      We'll also have a special place in the history books because we were the first species to write them.
- dekhn 8y ago
  Convergent evolution is a thing, it occurs, but it's generally considered super-rare due to the parsimonious assumption. It's unlikely that the sequences of the two independently evolved proteins would be so similar; you also wouldn't see a chain of progressively similar hemoglobins as you moved down the gene tree to older ancestral organisms.
  - joshuahedlund 8y ago
    > Convergent evolution is a thing, it occurs, but it's generally considered super-rare. Not anymore - though it depends on what precisely you mean by convergence, of course. I highly recommend the new book Improbable Destinies by Jonathan Losos[0] [0]https://www.amazon.com/Improbable-Destinies-Chance-Future-Evolution/dp/0399184929 https://www.amazon.com/Improbable-Destinies-Chance-Future-Ev...
    - dekhn 8y ago
      By convergence, I mean in the sense that two independent organisms that did not share a historical character trait (in this case, a specific homologous gene) independently evolved an identical trait (a gene with provably no homology, but identical function) through the process of natural selection, with no information sharing via horizontal gene duplication. This was argued out a while ago with stick insects that lost and then regained the ability to fly (several independent subspecies did this). A lot of people thought it meant the stick insects "completely lost all the genes associated with wing formation" and then "gained an entirely new set of genes that caused wing formation", but folks in the evo devo world believe- and I agree- that the insect never lost anything except a few regulatory domains that managed the expression of pre-existing components that are depended upon by multiple other subsystems (IE, wings are composed of basis proteins that are used for many body parts). My interest is in molecular evolution, not full character traits, because those phenotypes are incredibly complex and IMHO beyond our current level of sophistication in analysis.
      - joshuahedlund 8y ago
        > By convergence, I mean in the sense that two independent organisms that did not share a historical character trait (in this case, a specific homologous gene) independently evolved an identical trait (a gene with provably no homology, but identical function) through the process of natural selection, with no information sharing via horizontal gene duplication. I'm no expert and could be wrong but I think this is what Losos is referring to in his book. For example, "New and Old World porcupines do not share a common evolutionary heritage… The two lineages have independently evolved their quills from different, unquilled rodent species." Dozens of stuff like this. He goes into more detail with tropical island anoles, his field of expertise, and orients the whole discussion around Stephen Jay Gould and Simon Conway Morris's competing views on the overall paradigm of convergence. See this NPR interview for a quick summary[0]. A key quote (which I'm not discerning enough to tell if it challenges your claims or if your claims are actually already in response to these claims): "the flood of molecular DNA data that has come forth in the last two decades or so has in many cases revised our understanding about how species are related to each other. And it has revealed that many species that we thought were similar because they're closely related, that they're not closely related and that their similarity is the result of convergent evolution." https://www.npr.org/2017/09/07/549250035/biologist-jonathan-losos-explores-convergent-evolution-in-improbable-destinies https://www.npr.org/2017/09/07/549250035/biologist-jonathan-...
- searine 8y ago
  Yes, as other have said "convergent evolution" is a concept in biology. However, in the case of hemoglobin this is unlikely because this gene is particularly large, and sensitive to change. As a result it is highly "conserved". That is, mutations in this gene are selected against at a high rate because they tend to be deleterious. To create a gene like hemoglobin, you'd need hundreds of mutations to develop a hemaglobin gene from raw material. It is possible, but unlikely that humans and sharks would have independently accrued the same exact mutations in the same places since their divergence to create the same gene. It is far more likely that since this gene is essential, it has remained mostly unchanged since the divergence of sharks/humans from their common ancestor.
- fahadkhan 8y ago
  I believe it's called "convergent evolution". But I am not a geneticist, biologist,... https://www.sciencemag.org/news/2013/09/bats-and-dolphins-evolved-echolocation-same-way https://www.sciencemag.org/news/2013/09/bats-and-dolphins-ev...
- xenadu02 8y ago
  Everyone is right in a way. Evolution is messy and undirected. Some genes appear very early in the tree of life. Others have re-evolved two, three, or hundreds of times. This happens both because there may only be one reasonable way to encode the same function or because the same existing structure can be re-used for the same “new” function (evolution often re-uses existing features because that’s far easier then evolving ex nil)
- fastaguy88 8y ago
  There is a lot of confusion in this discussion (and in the original paper) about what "genes" are, and what "novelty" means. Human genes and shark genes (the DNA sequences) are not nearly identical, in fact, the DNA sequences that encode human and D. rerio (zebrafish, closer than a shark) hemoglobin share about 67% identity over about 2/3 of the mRNA coding length, which is which is quite statistically significant (expected 1 in 10^-30 by chance). But hemoglobin "genes" (the DNA) encode hemoglobin protein, and the human and D. rerio protein sequences share more than 50% identity over the entire length of the protein; a level of similarity expected by chance once in 10^45 searches (these low probabilities would be much much lower for an average length protein of 400 amino acid, globins are much shorter -- 145 aa -- so they have excess similarity or statistical significance). In the protein world, sequences with less than 30% identity often have very high statistical significance. As several writers mention, when the amount of similarity is so high that the odds of it occurring by chance are very low, the simplest explanation is that the similar sequences diverged from a common ancestor. Let me reassure you that computational biologists who do these kinds of analysis are very aware that evolution is not linear (hence the many methods for building evolutionary trees), and that similar mutations could (and do) occur in different branches of a tree. The argument being made here is that something new has appeared -- there are many new trees that emerged about 650 million years ago. (In the protein world, 650 million years is a relatively short time, so evolutionary relationships at that distance should be detected.) That said, it is very dangerous to talk about "novel genes" or "novel proteins" without being very clear about the nature of the novelty. Just as protein sequence comparison is more sensitive (has a longer evolutionary look-back time) than DNA sequence comparison, there are methods (not used in this paper) that can look back even farther, and we know that there are ancient evolutionary relationships that are difficult to recognize using sequence comparison, the approach used here. Moreover, many proteins are build from modules (called domains) that can be rearranged, so even though the module might be old, the particular arrangement might be newer. After a quick scan of the paper, it was unclear to me whether the authors are claiming that there are a large number of genuinely novel domains (unlikely), or simply arrangements (more likely), or perhaps simply duplications of existing genes (very likely, but not very novel).
  - chiefalchemist 8y ago
- pvaldes 8y ago
  > That means hemoglobin genes were already present in their common ancestor Or that some DNA capture happened in some part of the road. Now we have transgenic tomatoes with flatfish genes in their DNA. There is not any guarantee that the common ancestor of both species would had developped those genes yet at the time of the code fork.
Aardwolf 8y ago
"Of all the genes in the human genome, 55 percent were already present in the first animal." AFAIK, genes contain base pairs, and a base pair encodes 2 bits of information (computer engineering perspective here ;)) When they say 55% is the same, do they mean: 55% of genes have a similar structure and amount of basepairs, or do they mean: exact same values for the base pairs bit for bit? Like for example gene rs4778138 has an effect on eye color (handwavy first search result of snpedia for the example here). So if in two humans, this rs4778138 has a different value, do they consider both humans to have the same gene (because it is one that encodes eye color to some value in each case), or a different gene (because it encodes a different eye color)?
- carbocation 8y ago
  Generally, let's say that a gene is a stretch of DNA that encodes some functional product. That product might be a protein, or an RNA that performs some function. Think of these stretches of DNA as distinct entities that can be recognized by start and stop signals. If you say that 55% of the genes in the human genome were already present in the first animal, then you're saying that stretches of DNA which bear a significant similarity to 55% of ours were found in the first animal.
  - Retric 8y ago
    It's also far less profound than you might think as cells are extremely complex and don't have that much wiggle room. They hit a local optima after hundred of millions of years so it's a really good one. Not just copying DNA, but also a cell wall and nucleus etc. On top of that multi cellular organisms are on the evolutionary slow lane, they have smaller populations, take longer to reproduce, and don't simply hot patch any random bit of DNA they come across.
    - reubenswartz 8y ago
      This is a great comment and I agree almost completely. However, I think it’s very profound— it says something about the incredible power and versatility of cellular building blocks.
olivermarks 8y ago
What's the difference between an evolutionary biologist and a philosopher? There seems to be a lot of conjecture and theories here presented as fact...
- fifnir 8y ago
  Is it that people don't second guess everything a philosopher says ?
- searine 8y ago
  What conjecture? This is empirical. The researchers are observing the DNA from different orders of life (based on their extant species) and comparing them. They report their quantitative similarity. What about that is not factual?
  - d0100 8y ago
    The cause?
camjohnson26 8y ago
Anyone with an open mind should read Darwin's Doubt by Stephen Meyer. He looks at possible explanations for the Cambrian Explosion and concludes that Intelligent Design is the best explanation. Evolutionary Biologist Jerry Coyne has written a response to it. https://www.amazon.com/Darwins-Doubt-Explosive-Origin-Intelligent/dp/0062071483/ref=sr_1_1?ie=UTF8&qid=1525790601&sr=8-1&keywords=darwin%27s+doubt https://www.amazon.com/Darwins-Doubt-Explosive-Origin-Intell... https://www.forbes.com/2009/02/12/evolution-creation-proof-opinions-darwin_0212_jerry_coyne.html#6db6c86a3500 https://www.forbes.com/2009/02/12/evolution-creation-proof-o...
- dwaltrip 8y ago
  Unfortunately, "intelligent design" is not a scientific theory. It doesn't provide any method for categorizing life on Earth (e.g. what actually makes two kinds distinct), and it makes no concrete, specific scientific claims about how and why different forms of life are found in different parts of the world (here's an easy one: why do islands and other isolated regions have such unique life?). The list goes on. It's also disingenuous to ask people "to have an open mind" when the overwhelming weight of scientific evidence and consensus strongly supports evolution. There needs to be a damn good reason to bother looking at a lonely contrarian argument, especially as it has likely been debunked already.
  - whatshisface 8y ago
    This kind of meta-argument ("not a theory") rubs me the wrong way. It's a concrete claim about what happened (a mind much like ours but smarter made decisions about what stuff there should be, and then assembed it.) It can't be dispoven because no matter what you find you could say that it was just designed that way, but neither can evolution strictly speaking because there's the anthropic principle to reckon with (no matter how unlikely we were to arise, here we are. There's a nonzero chance of it all just tunneling together, and it's a big universe - if you could somehow show that our existence depended on a one in 10^9999999 chance, we'd just say that it happened.) Still, I feel that couching Christian or other religious faith in "theory" language is not completely honest. I don't think anyone really supports intelligent design, as opposed to Jesus speaking the world into being design.
brugidou 8y ago
À assez
dclowd9901 8y ago
"The new genes also proved to be remarkably durable. Of all the genes in the human genome, 55 percent were already present in the first animal." I read a line like that and I can't help but think of a Prometheus-style situation with the Earth and its species.
- SlowRobotAhead 8y ago
  Didn’t we all think that? ;)
  - dboreham 8y ago
    I've long wondered about this : if it can be shown that there isn't enough delta(t) in earth history for all of evolution to have happened, then some of evolution must have occurred somewhere else. Life, in at least some form, moving from other star systems seems at least not completely impossible.
    - SlowRobotAhead 8y ago
      Sure, but the issue is humans would be such an accident that you’d have to think we’d almost be considered an undesirable element or virus to whatever intentions a pollination device would have had. Hope they never come back to check on us, one look at Instagram and we’re gone.
      - noir_lord 8y ago
        Aliens: "What did you do?!, The Polar Bears are Brown" (paraphrasing Louis CK).
    - searine 8y ago
      Evolution functions on a model of "punctuated equilibrium". Lots of time doing nothing, with sporadic bursts of change. So there is more than enough time for evolution to occur, even on a drastically shortened earth timeline. Most of the time, life is just maintaining the status-quo, until outside factors tilt fitness in one direction and the system readjusts.
mmjaa 8y ago
Question for the serious: is this first animal not God?
- amerine 8y ago
  No.
- monocasa 8y ago
  Brings a new meaning to all of the 'god is dead' I see at punk concerts. So, haha, no.
- pc2g4d 8y ago
  Not in the traditional "uncaused cause" sense, but I guess you could spin it that way. Probably a better analogue would be Adam and Eve.
jonmc12 8y ago
Here are some related papers that speak to timeframes and adaptations related to these early animal genetics. Metazoa (760mya) - "animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle)" Eumetazoa (760-680mya) - "Characteristics of eumetazoans include true tissues organized into germ layers, the presence of neurons, and an embryo that goes through a gastrula stage." [1] Planulozoa (680mya) - "A 2004 study investigated the relationships between biradial and bilateral animals in evolution. If biradial is the link between radial and bilateral, then would seem to suggest that bilateralism occurred before cephalization. Called the Planulozoa Hypothesis, the authors suggests that ctenophora are the sister clade of bilateralians, and that all three of the groups – cnidarians, ctenophora and bilaterals – are the descendents of a single bilateral ancestor." [2,3] Bilateria (650mya) - "A Hox system is thought to have arisen (indicated by a red bar) after the divergence of the cnidarians from the common ancestor that gave rise to bilaterian animals (ecdysozoans, lophotrophozoans and deuterostomes)." [4] [1] https://en.wikipedia.org/wiki/Eumetazoa https://en.wikipedia.org/wiki/Eumetazoa [2] https://en.wikipedia.org/wiki/Planulozoa https://en.wikipedia.org/wiki/Planulozoa [3] http://biologicalexceptions.blogspot.com/2015/02/mirroring-evolution.html http://biologicalexceptions.blogspot.com/2015/02/mirroring-e... [4] https://www.sciencedirect.com/science/article/pii/S0960982206017787 https://www.sciencedirect.com/science/article/pii/S096098220... [5] https://pdfs.semanticscholar.org/3003/cc4844fe878fbe00167da6d8206d59a67f3c.pdf https://pdfs.semanticscholar.org/3003/cc4844fe878fbe00167da6... - list of gene adaptations by LCA.
dzonga 8y ago
I took this MOOC course, called Model thinking. One thing that blew me away was Cellular Automata. How complexity can arise from simple rules e.g Yes or No. From then I knew how simply evolution or 'creation' happened.

98 points by montrose 8y ago

"Humans and sharks, for example, make hemoglobin using nearly identical genes. That means hemoglobin genes were already present in their common ancestor." Um. If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? At two different times? At two different branches on the species tree? Not really my area but there seems to be an assumption that species development (dare I say evolution) was linear, with humans being the ultimate achievement in that process. But doesn't the fact that genes mutate - sometimes triggered by viruses - imply the process was not at all linear?

phito 8y ago
Convergent evolution is totally a thing. What if at some point in time, there was a virus running around and copy pasting some dna around?
- mannykannot 8y ago
  I think it is generally true to say that individual genes don't work in a vacuum, and neither do the biological mechanisms they encode for, so the transferred DNA would have to contain a suite of co-dependent genes. Admittedly, there is a counter-example in the transfer of genes conferring resistance to a particular pathogen. I think it is also true to say that convergent evolution often produces results that differ genetically, even though the resulting phenotypes serve the same purpose.
- fifnir 8y ago
  Check out these guys: https://en.wikipedia.org/wiki/Transposable_element https://en.wikipedia.org/wiki/Transposable_element
- stevenwoo 8y ago
  Like this retrotransposon? https://www.theatlantic.com/science/archive/2018/04/the-shellfish-gene/558131/ https://www.theatlantic.com/science/archive/2018/04/the-shel...
shawabawa3 8y ago
I'm not an expert in the field but my understanding is that DNA has a huge amount of "junk" in it. This junk doesn't do anything but can act as a fingerprint for where the DNA evolved from, as it's impossible for the junk to be evolved twice in exactly the same way
- jbrooksuk 8y ago
  I'm sure the "junk" DNA does something, we just don't know what yet.
  - perl4ever 8y ago
    Seems to me, "junk DNA" could be "commented out" code, which provides resilience to selection pressure, but doesn't technically do anything right now.
    - ethelward 8y ago
      That's pseudogenes, but it's not a massive part of the non-coding DNA.
- kingkawn 8y ago
  The concept of junk DNA was mostly taken apart a few years ago. Those sections often serve regulatory functions and other purposes related to controlling how genes are used and at what rates.
  - dekhn 8y ago
    You're referring to regulatory regions which really represent a tiny component of the genome (in terms of base fraction)... but nobody has really constructed a strong argument (that can be tested) that long stretches of Alu (which comprise most of the junk DNA) actually have a regulatory or other function. It's speculated those regions are gene foundries, but it's mostly speculation with limited evidence.
    - 8y ago
gort 8y ago
> Um. If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? At two different times? At two different branches on the species tree? Genes are long sequences of information. You could easily have quite different genes doing similar things, but if you have the very same gene (sans minor differences) it's just too unlikely to have originated completely independently twice. The closest thing I can imagine to your scenario is where, because of shared ancestry, 2 species have a certain gene, and then some minor mutation hits both of them, and now they both have some other gene. I suppose that's possible. But they already shared the original gene to start with.
- lkrubner 8y ago
  If a mutation in a given gene leads to death 99.9999% of the time, but leads to oxygen transport the rest of the time, and the mutation happens many millions of times, then it is reasonable to think it could have been invented twice. Most of the time the mutation leads to death, but every once in a million times it leads to a happy result. Over the course of a few million years, the mutation happens many millions of times. In that scenario you would expect to happen at least twice, and probably much more often. As an example, write a simple program that randomly generates strings of letters from 1 to 20 characters in length. Then include an English dictionary in the program. Compare the randomly generated strings with the words in the dictionary. How often does the random process generate actual words? Not often, but sometimes, and that is all that is needed.
  - gort 8y ago
    Sure, but this is only possible if the original (shared) gene was really quite close to being able to transport oxygen.
  - rlpb 8y ago
    What if there are a million different possible genes that produce hemoglobin? In that case, if two different species were found to produce hemoglobin but use the same gene, then what would that imply? I think this is what grandparent meant by "You could easily have quite different genes doing similar things".
zimpenfish 8y ago
> there seems to be an assumption that species development (dare I say evolution) was linear, with humans being the ultimate achievement in that process Only amongst people who haven't done any reading or learning about evolution. > the process was not at all linear Indeed. > If this gene was the result of a mutation, isn't it possible, at least in theory, that mutation happened more than once? Yes. But if the gene is nearly identical in sharks as in humans, the chance of that happening from convergent evolution would be small enough that "they have a common ancestor" is a much more likely cause.
- kevin_thibedeau 8y ago
  There is always the possibility of horizontal gene transfer mediated by a pathogen.
  - glenneroo 8y ago
    Mosquitoes supposedly helped transfer bits of DNA between species, which over millions of years influenced multiple species... or is that because they were the pathogen carriers?
huntertwo 8y ago
Evolution is not linear. All species are at a different leaf of the tree of evolution from some sort of “proto-being” as the root node. Humans are no different than dogs or cacti. Humans may be the common ancestor of two different species that exist 1 million years in the future. It is definitely possible that the two same mutations for hemoglobin happened at different points in time, but as I understand it, there is an assumption of parsimony. In other words, it is much more likely that the creation of genes for hemoglobin for sharks and humans happened at the same time than at different times.
- deleted 8y ago
  [deleted]
- PurpleBoxDragon 8y ago
  >Humans are no different than dogs or cacti. I think we will always have a special place in the history books (perhaps not a pleasant one) because we were the first to have some ability to consciously edit not only our DNA but the DNA of other species. Thinking about it, if life begin in millions of different universes, there would seem to be one of two possible outcomes. Life eventually goes extinct (due to something happening on the planet that life can't evolve to survive, if nothing else the death of the planet's star), or life develops a species with enough intelligence to be able to modify their own evolution. An idea similar to the anthropic principal. Though different in that we are a sufficient end case for the anthropic principal, but we haven't reached a sufficient end case in regards to evolution (though we have begun to grasp it).
  - lostapathy 8y ago
    We'll also have a special place in the history books because we were the first species to write them.
dekhn 8y ago
Convergent evolution is a thing, it occurs, but it's generally considered super-rare due to the parsimonious assumption. It's unlikely that the sequences of the two independently evolved proteins would be so similar; you also wouldn't see a chain of progressively similar hemoglobins as you moved down the gene tree to older ancestral organisms.
- joshuahedlund 8y ago
  > Convergent evolution is a thing, it occurs, but it's generally considered super-rare. Not anymore - though it depends on what precisely you mean by convergence, of course. I highly recommend the new book Improbable Destinies by Jonathan Losos[0] [0]https://www.amazon.com/Improbable-Destinies-Chance-Future-Evolution/dp/0399184929 https://www.amazon.com/Improbable-Destinies-Chance-Future-Ev...
  - dekhn 8y ago
    By convergence, I mean in the sense that two independent organisms that did not share a historical character trait (in this case, a specific homologous gene) independently evolved an identical trait (a gene with provably no homology, but identical function) through the process of natural selection, with no information sharing via horizontal gene duplication. This was argued out a while ago with stick insects that lost and then regained the ability to fly (several independent subspecies did this). A lot of people thought it meant the stick insects "completely lost all the genes associated with wing formation" and then "gained an entirely new set of genes that caused wing formation", but folks in the evo devo world believe- and I agree- that the insect never lost anything except a few regulatory domains that managed the expression of pre-existing components that are depended upon by multiple other subsystems (IE, wings are composed of basis proteins that are used for many body parts). My interest is in molecular evolution, not full character traits, because those phenotypes are incredibly complex and IMHO beyond our current level of sophistication in analysis.
    - joshuahedlund 8y ago
      > By convergence, I mean in the sense that two independent organisms that did not share a historical character trait (in this case, a specific homologous gene) independently evolved an identical trait (a gene with provably no homology, but identical function) through the process of natural selection, with no information sharing via horizontal gene duplication. I'm no expert and could be wrong but I think this is what Losos is referring to in his book. For example, "New and Old World porcupines do not share a common evolutionary heritage… The two lineages have independently evolved their quills from different, unquilled rodent species." Dozens of stuff like this. He goes into more detail with tropical island anoles, his field of expertise, and orients the whole discussion around Stephen Jay Gould and Simon Conway Morris's competing views on the overall paradigm of convergence. See this NPR interview for a quick summary[0]. A key quote (which I'm not discerning enough to tell if it challenges your claims or if your claims are actually already in response to these claims): "the flood of molecular DNA data that has come forth in the last two decades or so has in many cases revised our understanding about how species are related to each other. And it has revealed that many species that we thought were similar because they're closely related, that they're not closely related and that their similarity is the result of convergent evolution." https://www.npr.org/2017/09/07/549250035/biologist-jonathan-losos-explores-convergent-evolution-in-improbable-destinies https://www.npr.org/2017/09/07/549250035/biologist-jonathan-...
searine 8y ago
Yes, as other have said "convergent evolution" is a concept in biology. However, in the case of hemoglobin this is unlikely because this gene is particularly large, and sensitive to change. As a result it is highly "conserved". That is, mutations in this gene are selected against at a high rate because they tend to be deleterious. To create a gene like hemoglobin, you'd need hundreds of mutations to develop a hemaglobin gene from raw material. It is possible, but unlikely that humans and sharks would have independently accrued the same exact mutations in the same places since their divergence to create the same gene. It is far more likely that since this gene is essential, it has remained mostly unchanged since the divergence of sharks/humans from their common ancestor.
fahadkhan 8y ago
I believe it's called "convergent evolution". But I am not a geneticist, biologist,... https://www.sciencemag.org/news/2013/09/bats-and-dolphins-evolved-echolocation-same-way https://www.sciencemag.org/news/2013/09/bats-and-dolphins-ev...
xenadu02 8y ago
Everyone is right in a way. Evolution is messy and undirected. Some genes appear very early in the tree of life. Others have re-evolved two, three, or hundreds of times. This happens both because there may only be one reasonable way to encode the same function or because the same existing structure can be re-used for the same “new” function (evolution often re-uses existing features because that’s far easier then evolving ex nil)
fastaguy88 8y ago
There is a lot of confusion in this discussion (and in the original paper) about what "genes" are, and what "novelty" means. Human genes and shark genes (the DNA sequences) are not nearly identical, in fact, the DNA sequences that encode human and D. rerio (zebrafish, closer than a shark) hemoglobin share about 67% identity over about 2/3 of the mRNA coding length, which is which is quite statistically significant (expected 1 in 10^-30 by chance). But hemoglobin "genes" (the DNA) encode hemoglobin protein, and the human and D. rerio protein sequences share more than 50% identity over the entire length of the protein; a level of similarity expected by chance once in 10^45 searches (these low probabilities would be much much lower for an average length protein of 400 amino acid, globins are much shorter -- 145 aa -- so they have excess similarity or statistical significance). In the protein world, sequences with less than 30% identity often have very high statistical significance. As several writers mention, when the amount of similarity is so high that the odds of it occurring by chance are very low, the simplest explanation is that the similar sequences diverged from a common ancestor. Let me reassure you that computational biologists who do these kinds of analysis are very aware that evolution is not linear (hence the many methods for building evolutionary trees), and that similar mutations could (and do) occur in different branches of a tree. The argument being made here is that something new has appeared -- there are many new trees that emerged about 650 million years ago. (In the protein world, 650 million years is a relatively short time, so evolutionary relationships at that distance should be detected.) That said, it is very dangerous to talk about "novel genes" or "novel proteins" without being very clear about the nature of the novelty. Just as protein sequence comparison is more sensitive (has a longer evolutionary look-back time) than DNA sequence comparison, there are methods (not used in this paper) that can look back even farther, and we know that there are ancient evolutionary relationships that are difficult to recognize using sequence comparison, the approach used here. Moreover, many proteins are build from modules (called domains) that can be rearranged, so even though the module might be old, the particular arrangement might be newer. After a quick scan of the paper, it was unclear to me whether the authors are claiming that there are a large number of genuinely novel domains (unlikely), or simply arrangements (more likely), or perhaps simply duplications of existing genes (very likely, but not very novel).
- chiefalchemist 8y ago
pvaldes 8y ago
> That means hemoglobin genes were already present in their common ancestor Or that some DNA capture happened in some part of the road. Now we have transgenic tomatoes with flatfish genes in their DNA. There is not any guarantee that the common ancestor of both species would had developped those genes yet at the time of the code fork.

Aardwolf 8y ago

"Of all the genes in the human genome, 55 percent were already present in the first animal." AFAIK, genes contain base pairs, and a base pair encodes 2 bits of information (computer engineering perspective here ;)) When they say 55% is the same, do they mean: 55% of genes have a similar structure and amount of basepairs, or do they mean: exact same values for the base pairs bit for bit? Like for example gene rs4778138 has an effect on eye color (handwavy first search result of snpedia for the example here). So if in two humans, this rs4778138 has a different value, do they consider both humans to have the same gene (because it is one that encodes eye color to some value in each case), or a different gene (because it encodes a different eye color)?

carbocation 8y ago
Generally, let's say that a gene is a stretch of DNA that encodes some functional product. That product might be a protein, or an RNA that performs some function. Think of these stretches of DNA as distinct entities that can be recognized by start and stop signals. If you say that 55% of the genes in the human genome were already present in the first animal, then you're saying that stretches of DNA which bear a significant similarity to 55% of ours were found in the first animal.
- Retric 8y ago
  It's also far less profound than you might think as cells are extremely complex and don't have that much wiggle room. They hit a local optima after hundred of millions of years so it's a really good one. Not just copying DNA, but also a cell wall and nucleus etc. On top of that multi cellular organisms are on the evolutionary slow lane, they have smaller populations, take longer to reproduce, and don't simply hot patch any random bit of DNA they come across.
  - reubenswartz 8y ago
    This is a great comment and I agree almost completely. However, I think it’s very profound— it says something about the incredible power and versatility of cellular building blocks.

olivermarks 8y ago

What's the difference between an evolutionary biologist and a philosopher? There seems to be a lot of conjecture and theories here presented as fact...

fifnir 8y ago
Is it that people don't second guess everything a philosopher says ?
searine 8y ago
What conjecture? This is empirical. The researchers are observing the DNA from different orders of life (based on their extant species) and comparing them. They report their quantitative similarity. What about that is not factual?
- d0100 8y ago
  The cause?

camjohnson26 8y ago

Anyone with an open mind should read Darwin's Doubt by Stephen Meyer. He looks at possible explanations for the Cambrian Explosion and concludes that Intelligent Design is the best explanation. Evolutionary Biologist Jerry Coyne has written a response to it. https://www.amazon.com/Darwins-Doubt-Explosive-Origin-Intelligent/dp/0062071483/ref=sr_1_1?ie=UTF8&qid=1525790601&sr=8-1&keywords=darwin%27s+doubt https://www.amazon.com/Darwins-Doubt-Explosive-Origin-Intell... https://www.forbes.com/2009/02/12/evolution-creation-proof-opinions-darwin_0212_jerry_coyne.html#6db6c86a3500 https://www.forbes.com/2009/02/12/evolution-creation-proof-o...

dwaltrip 8y ago
Unfortunately, "intelligent design" is not a scientific theory. It doesn't provide any method for categorizing life on Earth (e.g. what actually makes two kinds distinct), and it makes no concrete, specific scientific claims about how and why different forms of life are found in different parts of the world (here's an easy one: why do islands and other isolated regions have such unique life?). The list goes on. It's also disingenuous to ask people "to have an open mind" when the overwhelming weight of scientific evidence and consensus strongly supports evolution. There needs to be a damn good reason to bother looking at a lonely contrarian argument, especially as it has likely been debunked already.
- whatshisface 8y ago
  This kind of meta-argument ("not a theory") rubs me the wrong way. It's a concrete claim about what happened (a mind much like ours but smarter made decisions about what stuff there should be, and then assembed it.) It can't be dispoven because no matter what you find you could say that it was just designed that way, but neither can evolution strictly speaking because there's the anthropic principle to reckon with (no matter how unlikely we were to arise, here we are. There's a nonzero chance of it all just tunneling together, and it's a big universe - if you could somehow show that our existence depended on a one in 10^9999999 chance, we'd just say that it happened.) Still, I feel that couching Christian or other religious faith in "theory" language is not completely honest. I don't think anyone really supports intelligent design, as opposed to Jesus speaking the world into being design.

brugidou 8y ago

À assez

dclowd9901 8y ago

"The new genes also proved to be remarkably durable. Of all the genes in the human genome, 55 percent were already present in the first animal." I read a line like that and I can't help but think of a Prometheus-style situation with the Earth and its species.

SlowRobotAhead 8y ago
Didn’t we all think that? ;)
- dboreham 8y ago
  I've long wondered about this : if it can be shown that there isn't enough delta(t) in earth history for all of evolution to have happened, then some of evolution must have occurred somewhere else. Life, in at least some form, moving from other star systems seems at least not completely impossible.
  - SlowRobotAhead 8y ago
    Sure, but the issue is humans would be such an accident that you’d have to think we’d almost be considered an undesirable element or virus to whatever intentions a pollination device would have had. Hope they never come back to check on us, one look at Instagram and we’re gone.
    - noir_lord 8y ago
      Aliens: "What did you do?!, The Polar Bears are Brown" (paraphrasing Louis CK).
  - searine 8y ago
    Evolution functions on a model of "punctuated equilibrium". Lots of time doing nothing, with sporadic bursts of change. So there is more than enough time for evolution to occur, even on a drastically shortened earth timeline. Most of the time, life is just maintaining the status-quo, until outside factors tilt fitness in one direction and the system readjusts.

mmjaa 8y ago

Question for the serious: is this first animal not God?

amerine 8y ago
No.
monocasa 8y ago
Brings a new meaning to all of the 'god is dead' I see at punk concerts. So, haha, no.
pc2g4d 8y ago
Not in the traditional "uncaused cause" sense, but I guess you could spin it that way. Probably a better analogue would be Adam and Eve.

jonmc12 8y ago

Here are some related papers that speak to timeframes and adaptations related to these early animal genetics. Metazoa (760mya) - "animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle)" Eumetazoa (760-680mya) - "Characteristics of eumetazoans include true tissues organized into germ layers, the presence of neurons, and an embryo that goes through a gastrula stage." [1] Planulozoa (680mya) - "A 2004 study investigated the relationships between biradial and bilateral animals in evolution. If biradial is the link between radial and bilateral, then would seem to suggest that bilateralism occurred before cephalization. Called the Planulozoa Hypothesis, the authors suggests that ctenophora are the sister clade of bilateralians, and that all three of the groups – cnidarians, ctenophora and bilaterals – are the descendents of a single bilateral ancestor." [2,3] Bilateria (650mya) - "A Hox system is thought to have arisen (indicated by a red bar) after the divergence of the cnidarians from the common ancestor that gave rise to bilaterian animals (ecdysozoans, lophotrophozoans and deuterostomes)." [4] [1] https://en.wikipedia.org/wiki/Eumetazoa https://en.wikipedia.org/wiki/Eumetazoa [2] https://en.wikipedia.org/wiki/Planulozoa https://en.wikipedia.org/wiki/Planulozoa [3] http://biologicalexceptions.blogspot.com/2015/02/mirroring-evolution.html http://biologicalexceptions.blogspot.com/2015/02/mirroring-e... [4] https://www.sciencedirect.com/science/article/pii/S0960982206017787 https://www.sciencedirect.com/science/article/pii/S096098220... [5] https://pdfs.semanticscholar.org/3003/cc4844fe878fbe00167da6d8206d59a67f3c.pdf https://pdfs.semanticscholar.org/3003/cc4844fe878fbe00167da6... - list of gene adaptations by LCA.

dzonga 8y ago

I took this MOOC course, called Model thinking. One thing that blew me away was Cellular Automata. How complexity can arise from simple rules e.g Yes or No. From then I knew how simply evolution or 'creation' happened.