Blogging the Origin

Chapter 2: Variation Under Nature

Here’s a project for a playful biology grad student with some time on his or her hands. Take chapter 2 of the Origin of Species, ‘Variation Under Nature’, and modernize the language. Toss in a few figures and some contemporary citations. Give the result a title like ‘A routemap for biodiversity research 200 years after Darwin’, put your name on it and submit to Trends in Ecology and Evolution. I’m not promising anything, but you might get lucky.

In his first chapter on domestic species, Darwin spent a lot of time worrying about questions that, thanks especially to molecular genetics, we now have an idea how to answer. In this chapter, his concerns and uncertainties are alive, well, and bothering researchers.

In retrospect that first chapter, with its pigeon-fancying and classical sources, looks old-fashioned — I felt like I’d gone from 1859 to 1959 in the turn of a page. Besides staking out the ground for population genetics, Darwin, in half-a-dozen dense pages at the end of the chapter, outlines many of the patterns in the diversity, abundance and distribution of living things that ecologists are still trying to understand.

***

It turns out that when Darwin talks about variation, he means two things. He uses the word in the sense that biologists use it today, to mean variability between the members of a population or species.

Naturalists, he says, see such variability as an irrelevance and an irritation, because if your goal is to define a species, variation is the last thing you want: “These individual differences generally affect what naturalists consider unimportant parts … It should be remembered that systematists are far from pleased at finding variability in important characters.”

Darwin argues that important parts — for example, the “branching of the main nerves close to the central ganglion of an insect” — do vary. And that this variation is signal, not noise: “These individual differences are important for us, as they afford materials for natural selection to accumulate, in the same manner as man can accumulate in any given direction individual differences in his domesticated productions.”

But as well as being the raw material of natural selection, Darwin uses ‘variation’ to mean the product of natural selection: the variation between species and varieties whose evolutionary history has already diverged. This is something closer to what we know think of as diversity.

***

This chapter’s lodestone is the idea there is no clear line between these sorts of variation: “I look at individual differences, though of small interest to the systematist, as of high importance for us, as being the first step towards such slight varieties as are barely thought worth recording in works on natural history.” And so on, to sub-species and species.

To explain the origin of species, Darwin first undermines the idea of the species. In his first mention of the Galapagos, he says that the island’s birds made him realize “how entirely vague and arbitrary is the distinction between species and varieties”.

The name species “is arbitrarily given for the sake of convenience to a set of individuals closely resembling each other”. He quotes many expert disagreements about what deserves to be called a species and what is a mere variety. This fluidity of species in space underpins his argument that species are also fluid in time.

***

The idea of the species is still slippery. Best known is Ernst Mayr‘s biological species concept: that you can assign organisms to the same species if they will breed together “in nature” to produce fertile offspring.

But it’s hard to test this for fossils. Also, most of the world’s genetic, biochemical and ecological diversity is contained in all those microbes that don’t have sex as we know it. You could go on appearances — the phenetic species concept — but that seems like a backward step, and it’s not much use for metagenomics, which fishes DNA out of the environment and measures diversity by sequence similarity.

More useful in such cases is the phylogenetic species concept — a species is a group of populations that shares a common ancestor, and is distinct from any other similar group. Although, again, seeing as we all share a common ancestor sooner or later, it’s tricky to know where you draw the line between groups. The microbial ecologist Jessica Green once pointed out to me that microbiologists typically put two cells in the same species if their ribosomal DNA is 97% identical. Applying the same criterion to primates, she says, and you’d be sharing a species with the ring-tailed lemur.

There are lots of other species concepts, but Darwin still seems spot on when he says: “No one definition has as yet satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species.”

Here’s some advice for anyone agonizing over creating a perfect, all-encompassing species concept: chill out. Pretty much any biological category you care to think of has fuzzy boundaries. Genomics is making the concept of the gene more problematic. Colonial, clonal and modular organisms, such as slime moulds, aspen, and the vast underground mycelia of some fungi, make the concept of the individual tricky to pin down. The giant mimivirus blurs the line between viruses and cellular life. There’s been a long debate over whether viruses themselves should be classed as living things. And it’s proved impossible to come up with a list of properties that unambiguously define life.

This does not mean that terms such as species, gene, individual or life are useless. In many or most cases it’ll be obvious whether the thing or group of things you’re looking at belongs in a particular category or not.

But it’s not a lack of ingenuity that has left us without perfect definitions for these things, it’s that such definitions don’t exist. What Darwin shows in this chapter is that if nature doesn’t fit into our boxes, the task is not to build a better box, it’s to work out what the uncertainty is telling us.

On Friday, things turn nasty, in the ‘Struggle for Existence’.

Comments

  1. #1 Christopher
    January 14, 2009

    Fortunately, the uncertainty told Darwin that ‘boxness’ isn’t a useful paradigm to contain the fluidity of variation. It soon starts to leak out as the corners get soggy…

  2. #2 JHB
    January 14, 2009

    This blog is a great idea!

    Re: this post, you probably know that Steve Jones has written a book called Almost like a Whale, which does very roughly what you suggest in the first paragraph here, but for the whole Origin. The match between Darwin’s ideas and modern data is good enough that Prof. Jones leaves Darwin’s end-of-chapter summaries largely untouched.

    Almost has its problems, but isn’t a bad read and is quite interesting to look at once you’ve actually read Origin…

  3. #3 Doogan
    January 14, 2009

    I really like how Darwin shuts down the idea that each species is a special act of creation so methodically in this chapter. I wonder what an ‘Intelligent Design’ believer would think of this chapter, or if it would just pass over their heads…

    Also, an interesting note about 16S rRNA similarity in Bacteria, Rosello-Mora and Amann (FEMS Microbiology Reviews 25:39-67) showed that all bacteria in their study with >70% similar genomic (total) DNA also had >97% rRNA similarity, which is another common proxy for bacterial species. Interestingly, there were many pairs of species who shared >97% rRNA but when their genomic DNA is compared, they were less than <70% similar (all the way down to about 10%)

    Just another thing to think about when asking yourself What is a species?

  4. #4 Doogan
    January 14, 2009

    (sorry, I should have previewed before I posted)

    …when their genomic DNA was compared, they were less than 70% similar (as low as about 10%!)

  5. #5 Donna B.
    January 14, 2009

    I am loving this series! I’m not a scientist, just a groupie, but I’ve been one for years. I read “Origin of Species” in the late 1980s and I remember it as a readable book. I’m surprised at the comments about it being difficult prose by a few.

    Maybe, back in the olden days when I was going to school, we were made to read more of that ‘kinda’ stuff. Heck, Darwin was a breeze compared to Emerson. For me, at least.

    Anyway, I’ve just scoured my bookshelves and Darwin isn’t on there, though I’ve still got books from before that time. I raised a litter of book thieves, but I’ve learned it’s just easier to get myself a new copy.

    I’ll have to catch up when Amazon delivers!

  6. #6 Gee
    January 15, 2009

    Priest Gregor Mendel and Georges Lemaitre were both very religious and shared many of the same ideas that todays Intelligent Desigher believers have. Most would agree they did a masterful job within there related fields. What would have happen to these two if they were force to work within the scientific community of today? I can only hope that this will change, as it was not long ago when church and science respected one another

  7. #7 tresmal
    January 15, 2009

    Mendel and Lemaitre were both catholics, therefore if they were alive and working in science today they would both probably be theistic evolutionists.

  8. #8 Gee
    January 16, 2009

    Evolutionary Creationism, Intelligent Design, Christian Darwinism, what ever you want to call it, was not the point I failed to make. I was just trying to state that people who believe that life was created by intelligent, have contributed immensely to our scientific understanding.

    Many agree the all time greatest contributor to today understand of the universes around us is Isaac Newton.
    I for one feel Isaac Newton was the greatest mind that ever lived. Moreover, to think today if he was cloned, then reborn in today’s scientific climate. He would not be allowed to develop his unorthodox Christian based theologies that lead him to his understanding of physics. SAD..SAD..SAD…NO Sadly today’s scientist chase off the Neo-Newton’s. Bill Gates an Intelligent Design proponent is just one of many examples.
    I believe that when a truly gifted mind is allowed to pounder the deepest meaning of life from all standpoints may in be, Hindus, Muslims, Christians, Buddhists, or Darwinist the results is a much granular understanding of life…

    However when I read comments like the one Doogan posted…

    “Darwin shuts down the idea that each species is a special act of creation so methodically in this chapter. I wonder what an ‘Intelligent Design’ believer would think of this chapter, or if it would just pass over their heads”…

    I am reminded why I pick another career.
    No, it didn’t fly over my head, his ideas create a personal challenge to think deeper and focus more diligently on my understanding of the worlds around me. Contrary to the sheep who accept it as truth, never challenging it and therefore learning the formula that leaded to the perspective.

  9. #9 Michael NJ
    January 18, 2009

    “This does not mean that terms such as species, gene, individual or life are useless. In many or most cases it’ll be obvious whether the thing or group of things you’re looking at belongs in a particular category or not.”

    I presume the utility of these terms is primarily in the ability to communicate with others. Are there any other overriding reasons to use them? Historic value?

    I’ve been wondering whether some alternative nomenclature could be used that would fit the data at least as well, if not better. Not being a biologist, I don’t know if something along these lines already exists (or I’m just talking out of my rear, for that matter!), but is there any attempt to categorise organisms according to some sort of DNA fingerprint? Would this be too limiting? As I understand it, any two organisms that are not closely related would have sufficiently different DNA to make some sort of such coding useful. Are there corner cases where the differences are fewer than would fit? Or am I simplifying the problem too much, and there are too many different ways of creating such a ‘DNA fingerprint’ to use as a meaningful tool?

  10. #10 John Whitfield
    January 21, 2009

    There is exactly the kind of thing you describe, Michael NJ. It’s called DNA barcoding, and it sorts animals into groups based on the sequence of a short stretch of mitochondrial DNA. Some advocate it as an alternative to traditional taxonomy for classifying and identifying species. Others object.

    But I don’t think the advocates of DNA barcoding see it as a species concept — more a handy tool. I’d expect there still to be contentious cases, whichever sequence you used. My point is that there are lots of things that look like a duck, flap like a duck and quack like a duck, and in such cases ‘duck’ is a useful label. But then you’ll find a few things that look like a duck, flap like a duck, and cluck like a hen. In such cases, let’s neither redefine duck, or pretend a quack is a cluck.

  11. #11 Michael NJ
    January 21, 2009

    Quite. I was envisioning something that was more specific than the somewhat vague and ill-defined (from Darwin’s description) nomenclature that we currently use. I certainly wouldn’t see it as a better method for everyday communication, but would it not be more specific? Sort of a Unique Identifier that also carried information about how it related to other organisms? Again, I presume I am coming from a highly regular digital background, and perhaps am missing some of the issues.

    Anyway, I’m somewhat glad someone else has already had the idea!

  12. #12 McKenzie Smith
    January 5, 2012

    Darwin talks about the different sides of variation, and I wonder how one can really tell the difference between natural and domestic variation. Besides completely controlled variation, now and days isn’t all variation because of something else. Species adapt to the changing world around them, but if those changes are caused by other people are those things really natural? Just something to ponder.

  13. #13 blayne astrof
    January 8, 2012

    I found parts in this post very interesting yet a little confusing still. It says that the reader felt like they jumped from 1859-1959 in the course of 1 page because of such complexity of ideas. In one part it was interesting to read a quote from Darwin “branching of the main nerves close to the central ganglion of an insect”, which i think is basically stating that there are similarities between species through their nervous system and that many species are more similar than we think.

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