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Sep. 22nd, 2019 12:20 am![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
silverflight8I've been trying to learn more about natural history, especially deep time, and I've been trying to read general books on the subject. I have a pretty decent grasp of the time scales now - that took awhile to grasp, since we're not great at really understanding the difference between 5 million, 50 million, and 500 million years, not to mention 5 billion. I also read a couple pretty good general popular science books on the subject.
I took a lot of science in high school but although the curriculum very good, we never did cover biological classification, taxonomy, etc. So I tried to find textbooks about cladistics, specifically. I am so interested in this reconstruction of the tree of life - and staggered at how much I don't know (and frankly what the field doesn't know) about the species that populate it. Even leaving aside most the tree, which is bacteria and archaea, where I know almost nothing, even the animal branch is very very full of things I still know nothing about, even when considering phylum level classifications. Cnidaria, I know they're sea dwelling and often jelly, but what are the defining characteristics? My god there are so many worm phyla! (At least I recognize Annelida). I think I've confused brachiopods and bryozoa. I can't deal with the number of species described in Arthropoda - it dwarfs every other animal phyla. And phylum is one step down from kingdom. On the tiniest branch! There is just so much detail that you could drown in.
I don't have access to an academic library anymore - I could get an alumni pass by paying money but I don't even live in the same country anymore - so I turned to ILL, which is one of the best things in the world. The site's kinda finicky to use so I just sorta guessed and ordered a few books. I ended up with Biogeography: an Ecological and Evolutionary Approach by Cox, and Species & Speciation in the Fossil Record edited by Allmon & Yacobucci. Unfortunately I ran out of time to actually read cover to cover but I did enormously enjoy both. I mentioned to someone at work how much I enjoy reading them, and it made me think of the difference in difficulty. Work isn't difficult. There is definitely work to be done, there can be challenges in figuring out how best to do it with the resources available, how we can optimize our processes, and of course lots and lots of detail to absorb, the firm handles billions in assets so risk & control etc blah blah blah, but it's certainly not a challenge in the same intellectual way that thinking about these problems are.
Biogeography is a textbook and arranged in that order, starting with more general questions of how ecology can be studied, what biogeography is, and so on. It was SO interesting. It talked about experimental methods - eg, at very zoomed in resolutions, how are these three terrestrial arthropods distributed in this Scandinavian forest (there was a specific study done, they trapped insects in pits) and what can it tell us about what they eat and how they live? On a broader level, what areas of the world are more ecologically productive and is there anything that links them? How do the distribution of the types of flora and fauna differ? How closely are different flora related on different continents, and why are they more closely related between these two than these other two? Why is there so much more ecological diversity in the tropics but it falls off a cliff as you move higher in latitude? These are all general questions which are thought provoking and which I haven't thought about, or at least haven't for a really long time.
I learned a ton of stuff and it also made me realize that the Pliocene was extremely recent. I said I had a pretty good grasp of the geologic time scale - but the Cenozoic, the most recent eon, is difficult, because, being more recent, there are so many more periods, and also so many of them start with P. and have -ene at the end. At least the Devonian and Triassic are easily distinguishable! But it's OK, I'll put some effort in and remember them. But the last glaciation was very recent, ending 2.5 million years ago, which is practically yesterday. And the effects of glaciation were very strong on the larger animals living in higher latitudes, while the tropics were pretty untouched. It was really interesting.
The chapter on Patterns in the Past (and the one extending the topic to the present) was closest to what I wanted, but here the textbook definitely has to take a step back because of the difficulty in identifying species in the fossil record - and the inability to make the same kind of analysis that biologists studying living/very recent species can make. More on this later, but the fossil record is tremendously incomplete and so many fossils can only be categorized using morphological details (size, shape, types of bones etc). Genome sequencing revolutionized so much of our classification, and changed many species' classification which was previously done by morphology. But you can't take DNA specimens for most of the geologic record - it's just too decayed and we don't have the methodology/tech to do it, yet, anyway.
Speciation was so entertaining. I use entertaining deliberately because it made me actually laugh out loud in parts. It's really a collection of essays from different authors about the species problem, and specifically how it interacts with paleontology - published 2016, so about fifteen years after Biogeography. There are general chapters and then more specific ones based on phylum, and those are animal phyla (not plant or bacterial/microbial). Allmon addresses this - it was deliberate as I think the evidence is more complete for animals at least.
The species problem is at the root a philosophical one - is it meaningful to speak about species and does the natural world actually have them, or are they a human construction? If it is meaningful, then how can we distinguish species? And for this book, since it's specifically focused for paleontology, how can the scientists working with fossils deal with this problem (and can they provide insight)?
The first question is trickier than it looks, since species change over time, no two individuals of a species are identical given genetic diversity, and some of the definitions don't work all the time. For example, the "if they cannot breed fertile offspring they are separate species" - a common textbook definition - is difficult to apply to life forms that asexually reproduce. Allopatric speciation, where species are split when a barrier comes between two groups, are helpful for identification, but not always detectable, and anyway there are species that split despite not being physically separated - there are examples of sexual selection leading to new species, despite overlap, like the cichlid fishes. Underpinning the difficulty is that it's not as though a species, even a living one, has one set of genes. Every individual has slightly different genes, because of mutation or recombination, and when the species is splitting - where is the line drawn? So instead of dealing with discrete data, you have a range of everything. Personally, I think the first question (do species actually exist) is an obvious yes, and the differences are both material and meaningful, but the application gets to be very, very fuzzy indeed.
Anyway, it was a fascinating read. What made me laugh is the exasperation that several of the authors, especially Allmon, clearly have about the subject. It's an enormously difficult problem. The actual definition is a problem. The application is an even huger one. And it's not like it's a problem at the fringes of biology - the ability to meaningfully define a species is central to the field, and if there isn't a good way to speak about it and have a standard about what constitutes a species, then a lot of fields are going to fall down. How can anyone meaningfully talk about ecological patterns without some kind of general consensus about what constitutes a species? How can you construct the tree of life or look at descent? And so on. Allmon speaks specifically about the Modern Synthesis, which is the 20th century's further development of Darwinism and genetics and the introduction of mathematical models - and how paleontologists can and should get involved. From what he writes, the synthesis has been mostly by biologists who study living species, including those who work in genetics, ecology, etc etc, but paleontology needs to be involved, because they are the only field who can provide the time element. Speciation is hard to observe because every species is always midway through one - but the fossil record can actually provide a record of what became of a species event (if we are lucky). But it's an exasperating problem because of course, the data set provided by the fossil record is really, really incomplete and very bad in a lot of data ways - for example, fossilization doesn't occur randomly, it is more likely for certain things like hard mineralized body parts (eg shells) and incredibly unlikely for others (species' lungs) or that rock is subject not just to weathering but to being turned back into magma as tectonics move continents around, so your fossils are just gone sometimes.
And even once you have them, trying to figure out what species this pile of fossilized bone is just itself a massive problem. There is no genetic testing for stuff millions of years back, and the Phanerozoic eon, the age of life big enough to see, starts about 550 million years ago. What can you do? Paleontology has to rely on morphology, the shape of whatever is preserved. Sometimes you can get lucky and get fossils of other things like trackways or waste or eggs. Modern biologists who study living species can collect many samples so then at least you can use math to look at population-level similarities, and assign some kind of meaningful cut off (hopefully). But what do you do if your evidence consists of only one specimen? Or maybe two or three similar ones, but you can't tell if it's one species or two? There are definitely a lot of species which are just unclassifiable or have a big question mark over them - even sorting them into big bucket categories, way bigger than just species or family.
I also read the chapter from a paleontologist who works specifically with fish - ichthypaleontology. And I've learned there's an index called the Catalog of Fishes, which is hosted by a Californian university and which is literally, a catalogue of fish that live today. It is not complete but there are about thirty thousand well-classified fish in there, and it's digitally hosted, and I can only imagine how useful it must be. Paleontologists working with fossil fish have no such thing, and the fossil record for fish, of course, extends back ALL THE WAY to the beginning of the beginning of the Phanerozoic, practically, so that's about five hundred million years to cover - a staggering amount of time. The author kept writing that they needed something like the Catalog to help the field. There are species identified off single specimens that haven't been reviewed since the first time they were published, in 1800s. There are undoubtedly duplicates, or one species too finely split (back to the problem of species - one species, or two, or more, or subspecies, or or or).
Speciation is very different in flavour to Biogeography because of the nature of the books. Honestly, Speciation went partly over my head; lots of the words were simply not defined because it's meant for biologists working in the field, and likewise the diagrams. It is extensively crossreferenced with papers I don't have access to (plus references like 'personal communication, 2014' which is clearly an email or maybe a chat). It is dealing with the application and new discoveries or rather how to make the new discoveries, whereas textbooks summarize the generally accepted ideas and knowledge and don't incorporate or mention these uncertainties.
I'd still like to get a good general grasp of the tree of life, as neither of these books actually had a good list. I kind of fear that a real list would just be too much information unconnected to anything - despite all of this, I'm not into this in order to memorize hundreds of phylum names or anything, that's not the point. But they were very interesting reading.
Back to ILL!
I took a lot of science in high school but although the curriculum very good, we never did cover biological classification, taxonomy, etc. So I tried to find textbooks about cladistics, specifically. I am so interested in this reconstruction of the tree of life - and staggered at how much I don't know (and frankly what the field doesn't know) about the species that populate it. Even leaving aside most the tree, which is bacteria and archaea, where I know almost nothing, even the animal branch is very very full of things I still know nothing about, even when considering phylum level classifications. Cnidaria, I know they're sea dwelling and often jelly, but what are the defining characteristics? My god there are so many worm phyla! (At least I recognize Annelida). I think I've confused brachiopods and bryozoa. I can't deal with the number of species described in Arthropoda - it dwarfs every other animal phyla. And phylum is one step down from kingdom. On the tiniest branch! There is just so much detail that you could drown in.
I don't have access to an academic library anymore - I could get an alumni pass by paying money but I don't even live in the same country anymore - so I turned to ILL, which is one of the best things in the world. The site's kinda finicky to use so I just sorta guessed and ordered a few books. I ended up with Biogeography: an Ecological and Evolutionary Approach by Cox, and Species & Speciation in the Fossil Record edited by Allmon & Yacobucci. Unfortunately I ran out of time to actually read cover to cover but I did enormously enjoy both. I mentioned to someone at work how much I enjoy reading them, and it made me think of the difference in difficulty. Work isn't difficult. There is definitely work to be done, there can be challenges in figuring out how best to do it with the resources available, how we can optimize our processes, and of course lots and lots of detail to absorb, the firm handles billions in assets so risk & control etc blah blah blah, but it's certainly not a challenge in the same intellectual way that thinking about these problems are.
Biogeography is a textbook and arranged in that order, starting with more general questions of how ecology can be studied, what biogeography is, and so on. It was SO interesting. It talked about experimental methods - eg, at very zoomed in resolutions, how are these three terrestrial arthropods distributed in this Scandinavian forest (there was a specific study done, they trapped insects in pits) and what can it tell us about what they eat and how they live? On a broader level, what areas of the world are more ecologically productive and is there anything that links them? How do the distribution of the types of flora and fauna differ? How closely are different flora related on different continents, and why are they more closely related between these two than these other two? Why is there so much more ecological diversity in the tropics but it falls off a cliff as you move higher in latitude? These are all general questions which are thought provoking and which I haven't thought about, or at least haven't for a really long time.
I learned a ton of stuff and it also made me realize that the Pliocene was extremely recent. I said I had a pretty good grasp of the geologic time scale - but the Cenozoic, the most recent eon, is difficult, because, being more recent, there are so many more periods, and also so many of them start with P. and have -ene at the end. At least the Devonian and Triassic are easily distinguishable! But it's OK, I'll put some effort in and remember them. But the last glaciation was very recent, ending 2.5 million years ago, which is practically yesterday. And the effects of glaciation were very strong on the larger animals living in higher latitudes, while the tropics were pretty untouched. It was really interesting.
The chapter on Patterns in the Past (and the one extending the topic to the present) was closest to what I wanted, but here the textbook definitely has to take a step back because of the difficulty in identifying species in the fossil record - and the inability to make the same kind of analysis that biologists studying living/very recent species can make. More on this later, but the fossil record is tremendously incomplete and so many fossils can only be categorized using morphological details (size, shape, types of bones etc). Genome sequencing revolutionized so much of our classification, and changed many species' classification which was previously done by morphology. But you can't take DNA specimens for most of the geologic record - it's just too decayed and we don't have the methodology/tech to do it, yet, anyway.
Speciation was so entertaining. I use entertaining deliberately because it made me actually laugh out loud in parts. It's really a collection of essays from different authors about the species problem, and specifically how it interacts with paleontology - published 2016, so about fifteen years after Biogeography. There are general chapters and then more specific ones based on phylum, and those are animal phyla (not plant or bacterial/microbial). Allmon addresses this - it was deliberate as I think the evidence is more complete for animals at least.
The species problem is at the root a philosophical one - is it meaningful to speak about species and does the natural world actually have them, or are they a human construction? If it is meaningful, then how can we distinguish species? And for this book, since it's specifically focused for paleontology, how can the scientists working with fossils deal with this problem (and can they provide insight)?
The first question is trickier than it looks, since species change over time, no two individuals of a species are identical given genetic diversity, and some of the definitions don't work all the time. For example, the "if they cannot breed fertile offspring they are separate species" - a common textbook definition - is difficult to apply to life forms that asexually reproduce. Allopatric speciation, where species are split when a barrier comes between two groups, are helpful for identification, but not always detectable, and anyway there are species that split despite not being physically separated - there are examples of sexual selection leading to new species, despite overlap, like the cichlid fishes. Underpinning the difficulty is that it's not as though a species, even a living one, has one set of genes. Every individual has slightly different genes, because of mutation or recombination, and when the species is splitting - where is the line drawn? So instead of dealing with discrete data, you have a range of everything. Personally, I think the first question (do species actually exist) is an obvious yes, and the differences are both material and meaningful, but the application gets to be very, very fuzzy indeed.
Anyway, it was a fascinating read. What made me laugh is the exasperation that several of the authors, especially Allmon, clearly have about the subject. It's an enormously difficult problem. The actual definition is a problem. The application is an even huger one. And it's not like it's a problem at the fringes of biology - the ability to meaningfully define a species is central to the field, and if there isn't a good way to speak about it and have a standard about what constitutes a species, then a lot of fields are going to fall down. How can anyone meaningfully talk about ecological patterns without some kind of general consensus about what constitutes a species? How can you construct the tree of life or look at descent? And so on. Allmon speaks specifically about the Modern Synthesis, which is the 20th century's further development of Darwinism and genetics and the introduction of mathematical models - and how paleontologists can and should get involved. From what he writes, the synthesis has been mostly by biologists who study living species, including those who work in genetics, ecology, etc etc, but paleontology needs to be involved, because they are the only field who can provide the time element. Speciation is hard to observe because every species is always midway through one - but the fossil record can actually provide a record of what became of a species event (if we are lucky). But it's an exasperating problem because of course, the data set provided by the fossil record is really, really incomplete and very bad in a lot of data ways - for example, fossilization doesn't occur randomly, it is more likely for certain things like hard mineralized body parts (eg shells) and incredibly unlikely for others (species' lungs) or that rock is subject not just to weathering but to being turned back into magma as tectonics move continents around, so your fossils are just gone sometimes.
And even once you have them, trying to figure out what species this pile of fossilized bone is just itself a massive problem. There is no genetic testing for stuff millions of years back, and the Phanerozoic eon, the age of life big enough to see, starts about 550 million years ago. What can you do? Paleontology has to rely on morphology, the shape of whatever is preserved. Sometimes you can get lucky and get fossils of other things like trackways or waste or eggs. Modern biologists who study living species can collect many samples so then at least you can use math to look at population-level similarities, and assign some kind of meaningful cut off (hopefully). But what do you do if your evidence consists of only one specimen? Or maybe two or three similar ones, but you can't tell if it's one species or two? There are definitely a lot of species which are just unclassifiable or have a big question mark over them - even sorting them into big bucket categories, way bigger than just species or family.
I also read the chapter from a paleontologist who works specifically with fish - ichthypaleontology. And I've learned there's an index called the Catalog of Fishes, which is hosted by a Californian university and which is literally, a catalogue of fish that live today. It is not complete but there are about thirty thousand well-classified fish in there, and it's digitally hosted, and I can only imagine how useful it must be. Paleontologists working with fossil fish have no such thing, and the fossil record for fish, of course, extends back ALL THE WAY to the beginning of the beginning of the Phanerozoic, practically, so that's about five hundred million years to cover - a staggering amount of time. The author kept writing that they needed something like the Catalog to help the field. There are species identified off single specimens that haven't been reviewed since the first time they were published, in 1800s. There are undoubtedly duplicates, or one species too finely split (back to the problem of species - one species, or two, or more, or subspecies, or or or).
Speciation is very different in flavour to Biogeography because of the nature of the books. Honestly, Speciation went partly over my head; lots of the words were simply not defined because it's meant for biologists working in the field, and likewise the diagrams. It is extensively crossreferenced with papers I don't have access to (plus references like 'personal communication, 2014' which is clearly an email or maybe a chat). It is dealing with the application and new discoveries or rather how to make the new discoveries, whereas textbooks summarize the generally accepted ideas and knowledge and don't incorporate or mention these uncertainties.
I'd still like to get a good general grasp of the tree of life, as neither of these books actually had a good list. I kind of fear that a real list would just be too much information unconnected to anything - despite all of this, I'm not into this in order to memorize hundreds of phylum names or anything, that's not the point. But they were very interesting reading.
Back to ILL!
