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I'm currently reading Nick Lane's excellent book, The Vital Question, which explores what we know about the split between archaea and eukaryotes, so this was an
by jdleesmiller 8y ago
I'm currently reading Nick Lane's excellent book, The Vital Question, which explores what we know about the split between archaea and eukaryotes, so this was an exciting article. This discovery is still one level below that split, within the eukaryotes, but the ongoing discoveries of more and more ancient branches suggests the tantalising possibility that we may one day find something even more ancient still swimming around somewhere --- a missing link from billions of years ago.
What strikes me about both this article and Nick Lane's book is that when I was in school the tree of life was presented as this thing that people had pretty much figured out. Since then it's been altered almost beyond recognition using genomics. I hope there are people still in school who read articles like this one and get inspired to get into this amazing area of research.
- notafraudster 8y agoIf I know nothing beyond high school biology about taxonomy and nothing beyond a reasonably educated layperson about biology generally, is "The Vital Question" accessible? If not, do you have an example of a well written but quick introduction to the subject matter. I occasionally read pop-culture articles about, e.g. the discovery of giraffe subspecies, and think about how I'd like to know more about both the human-focused taxonomy side and the evo bio speciation side, but I don't know where to start.
- jdleesmiller 8y agoI would say it's accessible, yes. My background is CS and math, and I have managed to follow most of it, though I have occasionally got lost on some of the chemistry.
- Radim 8y agoBill Bryson's "A Short History of Nearly Everything" is an amazing layman start. It's a little dated (the first edition came out in 2004!) but to be honest, if you're interested in a "human-focused" intro and how the concepts fit together, things haven't really changed that much.
- dmd 8y agoI really, really, really loathe Bill Bryson, because every time he touches on something I actually know about, there are invariably glaring, awful mistakes, including repetitions of urban legends and just the sort of 'facts' you'd expect to find on a "AMAZING TRUE FACTS" diner placemat. And so I'm real reluctant to read what he has to say about other fields, because I've got to assume it's all that bad.
- justinator 8y agoCan you list some examples (or are examples collected somewhere?)
- Radim 8y agoMany of the errors were corrected in later editions (it's been in print for 14 years!). You can see the original errata here: http://errata.wikidot.com/0767908171 http://errata.wikidot.com/0767908171 I leave it to your judgement whether this makes you "really, really, really loathe" the author :-) Note the book had 20 pages of just bibliography.
- amonavis 8y agoYou know this is a problem for the layman like me. I need to get educated on the general aspects of so many things in life. But with science and knowledge always progressing at a fast pace, the "truth" is always evolving. And this makes it a problem because I cannot be 24/7 invested in every single area of my interest, which are many. So I appreciate Jared Diamond and Bill Bryson because they make available to me (random person with a lot of interests but limited time) a quick overview of things, which I gladly accept at a high enough accuracy. It's sort of like Wikipedia, yes not the be-all-end-all reference but gets you started.
- dotancohen 8y agoYou've got to understand the purpose of those books. You, dmd, are not going to do anything with the knowledge gleaned from those books, except possibly one of two things: Peruse further study, or inspire others (usually children) to be interested in the field. The book opens up the field, the basic concepts of the field, and a bit of history of the field to you. You now have the tools to go off and either learn more or inspire others. You can even get into conversations and debates with those well-versed in the field. The book is a gateway into a field, not a path to follow in the field.
- matt4077 8y agoIf you have a background in IT, and are modestly comfortable with statistics, the following foundational paper on algorithms to reconstruct the tree of life from genetic data should actually be understandable: http://science.sciencemag.org/content/311/5765/1283 http://science.sciencemag.org/content/311/5765/1283 The statistics really only ever amount to Occam’s Razor, I. e. fewer differences in the genome means closer relationship. Edit: actually free full-text link: http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf
- notafraudster 8y agoI am a statistician (although as I confessed nowhere near computational biology), so, uh, yeah this is up my alley.
- matt4077 8y agoExcellent! I believe I remember a far longer version of the paper, and interactive widgets to explore the tree. Couldn’t find those right now and am on the road, unfortunately. In any case, the process consists of basically two steps: “Align” the DNA of all the species you have sequenced. That’s done using algorithms such as smith-waterman, which minimize the number of edits needed to go from one species’ version of a gene to another. That number defines a metric that measures all the distances between the species. So, Orang-Utan to Homo Sapiens may be, say, “450”, while Homo Sapiens to Ficus Benjamini is, say “12321”. (The difference may also be measured on the level of protein sequences. The process is basically the same, only that edits may be assigned different distance scores, because some result in more functional differences, while others are functionally “silent”. Evolutionary pressure would make the first rarer than the latter) The metric is unitless (I. e. It doesn’t allow translation into, say, “years since species diverged”. But it should fulfill the triangle equality). Once you have a (triangle) matrix with all the difference, all that’s needed to reconstruct a binary tree that maximizes plausibility, I. E. minimizes the sum of difference at each branching point.
- matt4077 8y agoOne more thing: Jared Diamond (of “Guns, Germs, Steel” fame) transferred the exact, same method to linguistics, using it to discover the ancestry of Pacific Islanders using features of their respective languages instead of letters of DNA. The result is both a tree of their (cultural) ancestry, and a map of their migration/expansion from island to island.
- iamphilrae 8y agoRichard Dawkins’ The Ancestors Tale is a great layman introduction, on par with Bill Bryson’s as mentioned a few posts up. I’ve read both. Both cover similar subject matter, but approach it from opposite chronological orders.
- rsync 8y ago"If I know nothing beyond high school biology about taxonomy and nothing beyond a reasonably educated layperson about biology generally, is "The Vital Question" accessible?" I have not yet read _The Vital Question_ but I have read his previous books and I highly, highly recommend: _Power, Sex, Suicide_ _Oxygen_ If I had to pick just one, it would be PSS.
- jhbadger 8y agoI'd avoid it because it is a rather misleading book whether or not it is accessible. Many people (but especially Carl Woese) led to our modern understanding of molecular phylogeny. Lane's main contact for his book was Bill Martin, who was a rival to Woese, which is fine, but the result is a story in which Martin made all the major discoveries and Woese literally gets one sentence. I'd strongly recommend Quammen's "The Tangled Tree" instead, which is a more balanced book.
- reubenswartz 8y agoIIRC, Woese gets a fair bit of credit in TVQ. Certainly far more than a sentence.
- reubenswartz 8y agoOnly bio class I took was in high school. The Vital Question is tricky in some places (I don't pretend to understand all of the details), but accessible, interesting, and one of my favorite books of the last few years. Of course, YMMV, but don't let that hold you back.
- sparkcc 8y agoaccessible!!
- yters 8y agoWhy is it still taught as a tree, then? That seems like a pretty big discrepancy to just be a matter of "simplifying". Would also be more inspiring to students to know there is so much more to discover, as you point out.
- klodolph 8y agoWell, chunks of it are tree-like and chunks of it have less well-defined structure. The tree still works very well. We still teach the Bohr model of the atom, too.
- gbrown 8y agoI never understood why we were taught the Bohr model. If it was a history of science class then maybe it would make sense, but IMHO it just lets students develop incorrect intuitions.
- klodolph 8y agoScience is not an accumulation of knowledge, science is a set of techniques for discovering new knowledge and testing it. So if a chemistry class just taught you the most accurate world view that teachers had at their disposal, it would be a failure. Understanding the history of science—experiments are done, new models are proposed, old models are overturned—is critical to understanding how to do science in a way that is perhaps less critical in some other fields. Besides, every other model lets students develop incorrect intuitions. Incorrect intuitions are still useful, and by letting students develop intuitions based on more obviously incorrect models like the Bohr model, you are teaching them the same skills they will need to use when they discared Lewis dot diagrams for molecular orbitals, or any other point in the future when established models are replaced. If you can't do that, you’re not doing science, and if you can’t teach people how to discard theories, you’re not doing a good job at teaching science. There is a tendency among the older generation (any older generation, at any given time) to complain about how their children are being taught wrong. Parents will pass onto their children a bunch of facts and skills, only to find out that schools teach something completely different. This is natural, of course. You can’t freeze a curriculum in time and still make it useful, you have to throw some parts of it out. But if you take students through the process of throwing something out, like the Bohr model, they’ll be more prepared for a changing future.
- im3w1l 8y agoImagine if there is something really ancient out there but it's dying because of global warming or something. That possibility makes me sad.
- seibelj 8y agoOver the last 1+ billion years the Earth has gone through many shocking events. Not just large changes in global temperature through ice-age and warming periods, but the atmosphere composition, asteroids, super volcanoes, and so on. If the ancient life form is still alive today after all of that, I doubt global warming would cause it to die.
- empath75 8y agoSurvivorship bias. Lots and lots and lots of organisms died out during each of those changes. That things have survived so long is a matter of probability not inevitability.
- seibelj 8y agoMy point was that a 2 degree change in the atmosphere now isn't so extreme for a 1+ billion year old organism as all the other history it has lived through. I'm not trying to brush off the impact of global warming, I'm just placing it in the context of 1+ billion years of Earth history.
- akiselev 8y agoThat's the point? Anything that has survived for a billion years in a form that could still be considered roughly the same organism or a close descendant must have a relatively stable biochemistry and gene pool that is capable of surviving an extreme range of environmental changes - as close as you can get to a holy grail in natural selection. Obviously its survival would not be inevitable; not even stars can survive their own age.
- lkrubner 8y agoYou have the math backwards. If there are events that kill 99% of everything and a million such events occur, then the survivors must be hardy in the face of shock. Global warming won't kill them; they've already been through incidents of far worse warming and cooling.
- ryan-allen 8y agoSchool should do this with other areas of science, I remember being taught about atoms and how 'absolutely true' it was that they were the smallest possible things, despite the fact it was known at the time that was not the case in other areas of research. It would have piqued my interest much more at a young age if we were taught 'this is what we have found out... so far!'. There's still so much left to discover!
- kashyapc 8y agoA small digression on Nick Lane's book: I gifted myself The Vital Question in 2015 December. While Lane writes quite effectively without any mind-numbing jargon, the book still has quite a bit of technical chemistry (understandably). After the excellent first 80 pages, it took me a lot more will power to plough through. :-) (I paused at page 112 and never got back. Thanks to this reminder, I'll resume again.) When I was reading the book on a plane, a seasoned biologist happened to be sitting next to me. When I said that it's the first book of Nick Lane that I picked up, he said: "I'd rather suggest you to pick up Laine's other book, Life Ascending, and then get back to The Vital Question." (Edit: Oops, bad me, just noticed that there's already discussion about the book's accessibility in this thread.)
- deleted 8y ago[deleted]
- burning_hamster 8y ago> pick up Laine's other book, Life Ascending, and then get back to The Vital Question As an ex-biochemist who has read both books, this is excellent advice.