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As I study biology and microbiology in college, the more I realize that taxonomy and phylogeny classification schemes are essentially bullshit. Bioinformatics a

• tshadwell 13y ago
  So how do you classify life?
  • burke 13y ago
    > ...compulsion to shove things into neat little cubbies... > So how do you classify life? I believe that's the point.
    • tshadwell 13y ago
      I'm sure the author means dislike for the current system for trying 'too hard' to classify life, not dislikes it entirely, or out goes our ability to describe life with words entirely, which I think you'll agree is a pretty important faculty.
  • pvnick 13y ago
    Are you asking "how do you define life?" or "how do you separate organisms from each other?"? Regarding either question, I don't think anybody has a good answer, and that's what's so fascinating, because it really seems to be a metaphysical question rather than a scientific one.
  • makmanalp 13y ago
    Do we really need to classify it down to 8 taxonomic levels? At the last few levels I bet it tends to get really arbitrary. Or, we could have a variable-depth tree. Make it more specific only when you need to.
    • quasque 13y ago
      It is variable depth - the main ranks also have ranks between them, with some denoted by super- and sub- prefixes to the major categories, and others of unnamed rank defined only by its position between two adjacent levels. The NCBI's taxonomy browser is good for exploring the various lineages, e.g. here is the data for humans: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&name=Homo+sapiens&lvl=0&srchmode=1&keep=1&unlock http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode...
  • baddox 13y ago
    I think the underlying point is that while humans have an extremely strong (and undeniably useful) urge to classify things into clean groups, not everything lends itself to being so classified. The human urge to classify things is what makes possible paradox like the sorites paradox.
  • colinm 13y ago
    1) Dead. 2) Alive. 3) Somewhere in between.
    • SilasX 13y ago
      1) non-life: rocks, water, sand 2) definitely life: animals, plants, fungi 3) self-replicating systems that stay far from equilibrium for a substantial time: hurricanes, fire, Benard cells, viruses
      • anigbrowl 13y ago
        3) One of those things is not like the others - the abstracted information and constructed envelope of a virus seems qualitatively different to me, since that structure doesn't depend on external factors for its basic coherence. +1 for mentioning Benard cells, did not know of those.
• EarthLaunch 13y ago
  There's no harm in defining and categorizing things. The harm would be in forgetting that categories should be based on reality, but don't define reality (a Platonic mistake). When new information blasts away an existing categorization scheme, then a new one does need to be made.
  • pvnick 13y ago
    I agree, and that's why I said "Modern classification schemes." The current system doesn't work, and bioinformatics is blasting it away at such a speed that it can't seem to keep up. The current response seems to be just bandage it up, like a novice PHP developer's first web app devolves into spaghetti code because he doesn't know what an MVC framework it.
• otisfunkmeyer 13y ago
  Perhaps the answer lies in tagging. Rather than a hierarchical categorization, everything is just tagged and thus searchable. That way you don't have to keep trying to fit everything into preexisting categories... Seems to be the direction most other things are heading as well.
• CreRecombinase 13y ago
  If you find phylogeny to be "bullshit", your biology and microbiology professors have truly failed you. Evolution by natural selection has produced the wonderful diversity that is life. Phylogenetic reconstruction is the tool biologists use to understand the history of all life on the planet. The fact that some living organisms engage in lateral gene transfer, or that there is no definition of species that perfectly applies to all living things is no reason to abandon perhaps the most fundamental and central pursuit of biology. Who we are as humans is inextricably tied to our mammalian, primate, vertebrate and multicellular ancestry, and we know this by virtue of the wonders of phylogenetics.
  • dnautics 13y ago
    well, they kind of are bullshit, in the same way that the bohr model is bullshit, and that quantum mechanics is bullshit, too. It's not REALLY what's going on, but rather a simplification that gets your feeble brain to the point where it can do something useful. You'll eventually learn a model that's less bullshitty, that gets you doing one slightly more useful thing, but it's still bullshit. It really is bullshit, but it is useful bullshit.
    • CreRecombinase 13y ago
      Still no. You'd be hard pressed to find any biologists left that would argue that discrete taxa exist, but whether or not humans are more closely related to chimps or gorillas is superbly knowable and certainly not "bullshit". Likewise, whether or not birds and dinosaurs constitute a monophyletic clade is not bullshit. Even with all the "exotic" stuff like endogenous retroviruses or whatever "exception" you think you can raise, the "Tree of Life" model still works very very well, it just complicates how the branching works.
      • Retric 13y ago
        Mitochondria are another clear example showing the tree of life model is broken. And all it takes is one counter example to show a model is bullshit.
• danmaz74 13y ago
  "Essentially, all models are wrong, but some are useful." George E.P. Box
• JunkDNA 13y ago
  There are a great many biologists and bioinformaticians who don't "get" phylogenetics. Please, please don't be one of them. I worked with some world class evolutionary biologists in the drug industry early in my career and I was blown away by how useful this often ignored corner of biology has become when married with modern bioinformatics techniques. Here's an example: let's say you're trying to develop a new drug against a virus. You can isolate huge numbers of the virus from infected individuals and sequence the DNA very cheaply. Using selective pressure analysis you can look for regions of DNA that are being selected for over multiple generations of the virus. Why? Because these might be important for survival. If your drug can target those regions of the protein, the virus will have an uphill battle mutating and creating resistance to your drug. Here's one more: You can use phylogenetic techniques on individual proteins to see how closely related they are. Why do this? Because if you're developing an antibiotic, you want to know that the bacterial version has a sufficiently large evolutionary distance from the human version. Now you can do this at scale for huge numbers of bacterial proteins and identify the ones with the biggest distance from their human orthologs. This allows you to identify bad antibiotic targets upfront before pouring all sorts of money into experiments (or at the very least, going into said experiments with your eyes wide open).
  • teej 13y ago
    This is frightening and fascinating at the same time. Thanks for sharing.
  • pvnick 13y ago
    I actually agree with you regarding bioinformatics, and the subject you describe is one which I'm exploring as a career path. I was describing an indictment of classification schemes, not bioinformatics, and it seems there are plenty of respondents here that have misunderstood me. Which I suppose is either an indictment of the care with which I constructed my original comment or a lack of attention to the other comments I've made in this thread. Edit: Also, hi Mike!
  • ronaldx 13y ago
    > if you're developing an antibiotic... Beautiful examples in theory, but blown out of the water in practice. In the current age of bioinformatics, practical modern antivirals and antibacterials are not being identified, not at all[0]. As such, I find it awkward and outdated to claim that novel drug discovery is a great testament to phylogenetics and bioinformatics. Can anyone offer a practical example of how bioinformatics has genuinely been (pref. statistically) useful in successful drug discovery? I would also be interested in evidence that existing antibioitics could have been discovered more effectively, using new methods ab initio. [0] e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095086/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2095086/ "the success rate of discovery has gone down"
• mathattack 13y ago
  Growing up it seemed crazy having to memorize these arbitrary taxonomy schemes when things intuitively didn't seem so black and white. I guess every model has it's shortcomings.
• tokenadult 13y ago
  Are you studying those topics as a biology major, or as a student of some other major subject? There actually is a lot of criticism among biologists about how far behind the textbook representation of those topics is compared to the professional literature of biology. If "cladistics" is not a familiar term to you from your undergraduate education, that would be diagnostic of a poorly designed biology course, for example. See http://www.evolution-outreach.com/content/6/1/11 http://www.evolution-outreach.com/content/6/1/11 for a discussion of this issue and other issues about problems in biology education.
• arkades 13y ago
  To my understanding the classifications tend to be "lies we tell to children", much like the simplified atomic models sold to first-year chemistry classes. If you're a biology major, you never really need to get the Chemistry PhD's version of atoms, right? Very broad classifications tend to be useful, in that by definition they group similar organisms. Beyond that level of detail they're useless, yes, but beyond that level of detail you're already going into the level of expertise where you're expected to recognize their uselessness. Cell Biology PhDs may or may not realize it, but they're working on tyrosine kinases, not classifications.
• wissler 13y ago
  It's not "bullshit", it's just doesn't come with the same kind of guarantees that religion does. Our knowledge is refined and expanded over time. This is perfectly natural. The problem is when people are taught in an authoritarian manner, and then they run into places that method breaks down, and so throw the baby out with the bathwater. As you have done.
• jergosh 13y ago
  > Modern classification schemes are so arbitrary and error-prone as to be essentially just a painful way to satisfy scientists' compulsion to shove things into neat little cubbies and has the negative side-effect of scaring students away from an otherwise fascinating subject. What do you mean by "modern classification schemes"? If anything, molecular phylogenetics helped clarify earlier attempts at classification which used common morphological features.