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Single-base changes, or singletons?

  1. Jun 11, 2016 #1
    The May 20, 2016 issue of Science, p876-7, "Tracking how humans evolve in real time," subtitled, "Analyses of thousands of sequenced genomes show changes in as little as a generation," uses the term "singletons" in the 4th paragraph:

    "...single-base changes...or singletons..."

    My limited understanding presumes that a "single-base" change is one base in an allele.

    I cannot find a single reference on the net or in the many papers in my files on the subject of genes or genetics which use the term "singleton" by itself.

    I would like to be able to more broadly understand what the author is specifically intending or referring to with "singletons," and what other terms might be inclusive of the author's intentions in using "singletons," such as SNP.

    Or, are SNPs distinctly separate from anything relevant to "singletons?"

    Are "singletons" synonymous or related to "point mutations?"

    I believe that with most forms of science, the terminology is exponentially accelerating beyond any hope of an up to date glossary or reference, and we are enslaving ourselves in a form of ignorance by preferring single word definitions (that we can lay claim to for the enhancement of our status) of much that is actually complex, without providing a clear context. I hope I'm mistaken about that.

    Any links to relevant articles which will provide me with more understanding of "singletons" related to genes will also be appreciated.
     
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  3. Jun 12, 2016 #2

    epenguin

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    Maybe this http://learnernote.blogspot.co.uk/2015/03/tag-snp-and-singleton-snp.html explains and gives context and a relevant link.

    Your reaction about terminology is quite natural at least. However someone may find he is using the same concept repeatedly and having to make frequent tedious repetition of the same phrase, and searches for a short term to stand for the idea instead. But the term might look different to the person who is inventing and using it all day and every day than it does to anyone else. A term that is relatively self-explanatory is best. 'linkage disequilibrium'is so, "singelton" at first sight is not IMHO. Could you think of a better one?
     
  4. Jun 12, 2016 #3
    If all the author intends to refer to by her use of "singleton," is "single-base changes," then if it hasn't already entered the conventions, I would suggest the author follow the first use of "single-base changes" with (sbc)--especially given your affirmation that "singleton" is used with SNP. It also remains to be evaluated or understood by me whether "singleton" is also used (often or otherwise) with "point mutations."

    I chose to go "gently" with my suggestion of "sbc" because http://www.acronymfinder.com/SBC.html contains "only" 414 meanings for "SBC."

    Now a bit about "meaning," as I contemplate it: I believe that even with the expansion of a term--using two words--humans can continue to invent potential "rabbit holes."

    I had to find my way into "linkage disequilibrium," another of the so-many concepts that the virtually infinite subject of genetics contains, or will contain: Evolutionary change and our "learning curve" will never end, unless we become extinct or the universe closes up shop, right?

    And how many times does the history of science show that there are "corrections" needed, sometimes 180 degrees of change in meaning.

    Now, I may have to apologize:

    the definition of "linkage disequilibrium" as I read it makes sense, but--to me--only if we keep that definition but change it to "linkage equilibrium."

    "Disequilibrium" means "a loss or lack of equilibrium or stability."

    As I read about "linkage disequilibrium," it seems that if there is a "stable" link or "statistical associations" between alleles at different loci, then there is, revealed, a "stable" relationship between them, i.e., they are in "association," however initially unapparent, which means to my mass of gray matter that they are revealed to be in "linkage equilibrium." Revelations of this kind bring forth equilibrium, functional relationships.

    I just can't get my head around how some things that are in "stable, statistical associations" can also be in "disequilibrium," even though I can grok the intention that because they don't live in the same neighborhood, they don't appear to have a natural association. But forcing "closeness" to be the natural way-- the natural path to discover meaning--feels to me like an eventual normative trap into reductionism.

    Or, as I contemplate further, perhaps "disequilibrated associations" or "disequilibrated linkage" might work better, since they appear, initially, to have no functional relationship. In this type of terminology or conceptualization, it feels more sensible to me that the last word in the term puts you in the right order or direction. The first word refers to the "sensible" first take, but the second term redirects and concludes with the argument as intended. Or have I made my own rabbit hole with that one?

    I appreciate your affirmation of my reaction to "singletons" as "natural," natural at least on the planet I live on ~<;)

    Thanks for joining my very first adventure on this part of the planet.

    Any clues to where the evolutionary break was between penguins and corvids?
     
  5. Jun 13, 2016 #4

    Fervent Freyja

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    Sometimes an article will introduce a known term like "single-base changes" alongside a new term "or singletons" as an indicator that the terms have the same meaning but may be a signal that the introduced term will probably be used throughout the article instead.

    This paper uses the term "singletons" to compare evolutionary rates with "duplicates". I think that terminology in cases like this are good attempts to keep the paper clear and improve communication of those results.
     
  6. Jun 14, 2016 #5
    If I understand the use of "singletons" in the paper you refer to, the authors were interested in comparing "orthologs that have paralogs (duplicates) and those that do not (singletons)."

    The paper looks interesting, but it is not, as a whole, appropriate for me to study in depth, at this time, but the additional example is a big help.

    A primary need I have is to find resources for discussion about a wide range of terminology in many of the sciences and humanities in order to begin pulling together 30 years of my independent research across many disciplines. Which is why I made my first post here.

    While authors like Bruce Alberts make cell biology highly accessible for me and I can readily begin to make hypothetical connections or analogs with other disciplines, I avoided the study of genes--for the most part--because it seemed to me that for many decades there still wasn't sufficient agreement about the definition of a gene. Meanwhile research in "genes" grew exponentially...and then there came "epigenetics," another term that means so many different things to different authors, aside from the two basic categories of in vivo development, and now what may be a never-ending investigation of epigenetic phenomena in development following birth. I give that as a context example.

    My OP refers to an article where I "think" the author was focusing on "single-base changes." In the paper you link to (cited 164 times since 2004), the authors are using "singletons" in reference to whole genes (whatever they are...;). I find that "singletons" is a term also used when comparing against twins. Stanford Encyc. of Phil. lists 52 papers using the term "singleton," yet the Oxford Companion to Philosophy (1st ed.) does not seem to touch on the term.

    My dream is that somewhere, somehow there will be established a "UN" for certifying conventions of philosophical, scientific, and psychological terminology--not agreement about "what" specific terms mean, but conventions of language and concepts so that people can understand what phenomena they are discussing.

    I haven't received any specific comments about the specific paper and usage I was confused about, so I still don't know if anyone is sure that the author of the paper in question in my OP "only" intends using "singletons" in reference to "single-base changes" or if, for example, "point mutations" or SNPs would satisfy her argument or not.

    My starting point is exemplified by the philosopher, PMS Hacker in his 2009 paper, "Philosophy: A Contribution, not to Human Knowledge, but to Human Understanding."

    Hacker's fundamental argument is that we cannot begin to discover "knowledge" (and I suggest about genes or anything else) without an adequate approach to "understanding," which requires a clear establishment of whatever relevant concepts there are which are fundamental to whatever one is studying (and hopefully some conventions of language for the discipline so that other people outside the "club" might gain a few clues).

    Hence, language and some "clues" to whatever conventions might exist--or not--for the use of "singletons" in biology and genetics. With the "twins" subject I discovered, and now the "orthologs that have paralogs (duplicates) and those that do not (singletons)" subject, I think I'm making some progress in understanding that "singletons" can be a general term that authors might apply to virtually any subject where there are more than just "singletons"...but I'm still in the dark about the OP paper, which seems to point to a potentially valuable change in the actual rates of evolutionary change. And it might be valuable to understand--for me, anyway-- if any or every form of "single-base changes" are relevant to that new potential perspective on actual rates of evolutionary change. For me, the paper winds up being about "singletons," rather than better informing me about what is more comprehensively or clearly relevant to a potentially new perspective on the actual rates of evolutionary change.

    Thanks for the reply and the link.
     
  7. Jun 15, 2016 #6

    epenguin

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    I think the meaning of the word 'singelton' in the work quoted by Freyja is completely different from that in the one you cite.

    My opinion is that "singelton" Is just a fairly generic word of English, so users of it in different areas will have different ideas in mind. Bridge players have one for 'singelton' for example.

    For your idea of a UN to rule in terminology I think it already exists to all the extent that it is useful in the various bodies like the International Unions. For xample the terminology of chemical structures is very developed and rigid. An example I am more familiar with is the Enzyme Commission. These reined in variation that did exist. Frankly I think this helps the computer more than human beings, and the different usages of the past were a slight nuisance, never all that much a barrier to communication. That you can or that it is any use trying to do this for evolving scientific concepts at an early stage like what you cite seems to me questionable. I'd guess this goes against the nature of discovery and evolution, and against the nature of language. This nomenclatural work seems to me less philosophical than is dictionary compilation.

    I do not at present have access to the journal and article you cite. However it looks to me that saying single base changes and 'singletons' are the same thing is like saying money or currency and 'dollar' are the same thing - the last is a particular kind of the first.

    There is no need to have such misunderstandings of the meaning of linkage disequilibrium that you show - you can very fast find plenty of articles on it, for example Wikipedia. Equilibrium/disequilibrium here is very similar to that in chemistry or physics. You could call it mixing. An allele a, say and an unlinked allele b will be distributed in individuals in a population just in the proportions you would calculate from simple probability - e.g. If the frequency of a and unlinked b are both 1%, then you will find them together on only 1/10,000 chromosomes. If instead, at the other extreme they are very closely linked, then they travel together and nearly every chromosome that is a is also b. It is stable in the sense that most progeny from a parent in who is a are also b. And the same for most of their immediate descendants. In that sense you can call it 'stable'. But 'most' is not 'all' - in fact due to a process called crossover, breaking and recombining different chromosomes happening in a more or less small fraction every generation, the close association dissolves over time, and the frequency that a and b are found together becomes that of the probability as per my example above. They equilibrate, mix, randomise, previously they were in disequilibrium. The more recent the mutation creating a or b the greater the disequilibrium. Thus you can trace aspects of human or other biological history over millennia - the paper seems to be something about that..
     
    Last edited: Jun 16, 2016
  8. Jun 16, 2016 #7

    Fervent Freyja

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    Now I see your angle. You are interested in the overall developments of knowledge in biology and how the current disorganization of concepts and terminology can affect student learning outcomes (comprehension)? This is certainly an admirable dream! There has been a great need for better guidelines and regulation of information exchange in biology. I do know that basic ideas and terminology are already internationally regulated for mathematics, chemistry, and physics, though I cannot recall the committees name!
     
  9. Jun 16, 2016 #8

    epenguin

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    Yes, most scientists know there are these regulations and probably don't know who makes them. Another example comes to mind, every animal species known to science gets an official name. This is of very long standing. Somebody must be keeping it continually under review, as not only are new species discovered but what was previously thought to be two different species turns out to be one, and vice versa.
     
    Last edited: Jun 16, 2016
  10. Jun 16, 2016 #9

    Fervent Freyja

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    There is not one person or agency regulating biological classification. Phylogenetic modeling seem to be more a free-for-all (pick what you want). Many people that work on optimizing tree-building methods have little background in biology. Many of these models have very different classification guidelines can end up looking entirely wrong when a different method is used.
     
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