Evolving Thoughts

What is a species?

If somebody asked me to write a short essay giving an overview of my favourite topic, the nature of species, I doubt that I could. I can write a long essay on it (in fact, several) but it would be excruciatingly hard to write a short one. For that, we need a real writer. Carl Zimmer is the guy. He has an essay on species in the current edition of Scientific American. And despite quoting some obscure Australian philosopher, it is a good summary of the issues. How he manages to get up on a topic like that amazes me. It took me a good five years.

There’s a connection with this blog. A while back I wrote on microbial species, which became a paper in History and Philosophy of the Life Sciences, after being a talk at a Microbiology conference in Exeter. As a result, Carl became aware that species conceptions was my thang, and so he called me up and we talked for an hour or so on his dime. I hope that I was helpful.

The essay has the following subhead:

The debate over species definition is far from over and is more than a mere academic spat. Proper classification is essential for designating the endangered list.

This is perhaps the most crucial aspect of the species concept debate, but it isn’t the most theoretically interesting. Biology, like most sciences, has a need for units of measurement. And like most sciences those units need to be grounded in the real world. So what species, the “rank” of biology that it is agreed on most sides is the most or only natural one in the Linnean hierarchy, are determines many measures of biology in fields from genetics to ecology. If, as a significant number of specialists think, the rank is a mere convention, then those measures become arbitrary and meaningless.

So, what sort of “unit” might a species be? I can think of three alternatives. One is that species are, in fact, simply a matter of convention, which is to say something that makes things convenient for us in communication, just as John Locke said in the Essay (although that was about the logical species, not the biological one). Instead, say researchers like Paris polychaete specialist Frederick Pleijel and Rutgers geneticist Jody Hey, we need to replace the notion species with something like a “least inclusive taxonomic unit” (LITU, Pleijel) or “evolutionary group” (Hey). There are other replacement concepts in the offing. And the so-called “phylogenetic species concept” is not really a concept of species, at least in one of the versions under that name, so much as something very like a LITU that gets called a species.

But there always have been replacement terms for “species” available. Even Linnaeus had a rankless taxonomic concept, cohort, and taxon itself was first of all a rankless concept. And always those terms end up being replaced by species anyway. Even “deme”, now a core term of population genetics (roughly meaning the local breeding population) was originally a rank-free term that got subverted. So I think that no matter what we think about ranks, we will continue to talk about species.

The second alternative is that species is a term that plays a theoretical role in biology, and this seems intuitively right: we talk about species as the units of evolution, so they are supposed to be required by evolutionary biology, and likewise in ecology, species are the unit that is crucial in defining the biodiversity of a region or ecosystem.

But if species are theoretical objects, we ought to find them as a consequence of theory, not as a “unit” that we feed into theoretical or operational processes, and so far as I can tell, this is not the case. Population genetics and evolutionary theory have populations, haplotypes, alleles, trophic nodes, niches and so on, but what they do not have are species. In every case where species are used in theory, they are primitives, or stand as surrogate terms for the things mentioned. Theory does not define species.

This might be challenged by adherents of Mayr’s biological species concept, or one of the derivative or related conceptions – a species is a protected gene pool, as Mayr said. This is certainly the view of Coyne and Orr in their Speciation book of a few years ago. But as Zimmer’s piece points out (and quotes me among others as pointing out) the vast bulk of life would not be in species if that were the case, and anyway, species were well described and identified long before genetics was developed, some two centuries before. So they must at least be things that can be observed in the absence of theory. Of course, some species are harder to identify than others, requiring techniques that are recent, but that still doesn’t make species theoretical objects.

This brings me to my third alternative: species aren’t theoretical objects at all; they are objects that have phenomenal salience. That is, we do not define species, we see them. Consider an analogous case: mountains. Mountains are hard to define, and they have a multitude of geological causes, ranging from uplift, subduction, vulcanism, differential erosion, and so forth. “Mountain” is not a theoretical object of geology – subduction zones, tectonic plates, and volcanoes are. A mountain is just something you see, although there are no necessary sets of properties (or heights) that mountains have to have, and it is often vague when differentiating between them. A mountain calls for an explanation, and the explanation relies on theory, but equally so do mesas, land bridges, and caves.

So my answer to the question Carl proposes: what is a species? is that a species is something one sees when one realises that two organisms are in the same one. They are natural objects, not mere conveniences, but they are not derived from explanations, but rather they call for them…

Comments

  1. #1 Matt Silb
    May 29, 2008

    And despite quoting some obscure Australian philosopher …

    Must be you, there aren’t any other obscure Australian philosophers, are there? If there are, I don’t know about them. ;-)

  2. #2 Jud
    May 29, 2008

    The very difficulty of making species classifications is a refutation of ID/Creationism. In ID, assistance beyond natural evolution is needed to transcend species “barriers,” i.e., to go from micro- to macro-evolution. In more classical Creationism, organisms are created as distinct unchangeable “kinds.” In such a neat and tidy world, there’s no reason for the existence of living things that are difficult to classify.

  3. #3 RPM
    May 29, 2008

    So my answer to the question Carl proposes: what is a species? is that a species is something one sees when one realises that two organisms are in the same one.

    What level of understanding of the organisms must one have before one can realize “that two organisms are in the same one”? Because there are a lot of organisms that, upon looking at them, one may conclude are the same species. However, these organisms are more different from each other than humans are from chimps. I think it’s the species concepts (whether it be phylogenetic, reproductive, or something else) that allow us to reach that realization.

    That’s not to say, of course, that species concepts are human constructs.

  4. #4 bob koepp
    May 29, 2008

    Jud – While not wanting to give any encouragement to advocates of special creationism, I don’t think they need to lose any sleep over the “species problem”. I figure they’re in pretty much the same situation as any of us who think “species” of furniture are the products of intelligent creators. Chairs, tables, etc, are similar to organic species in being difficult to classify. In other words, “difficulty of classification” isn’t evidence that something wasn’t created by an intelligent agent.

  5. #5 Jerry
    May 29, 2008

    So species, like porn, is something you can’t define but you know it when you see it? That would certainly fit the Latin origin of the word (something seen, appearance).

    An observer-centered definition based on the appearance of similarity can certainly elucidate the human use of the word species, and is perhaps particularly good at explicating its lack of stability. But it seems useless to account for the existence and perseverance of a natural character/trait set, where the critical question seems to be: how is change being stopped and for how long?

  6. #6 Eamon Knight
    May 29, 2008

    A SciAm article by Zimmer that mentions both Wilkins AND Algonquin Park? (about two hours up the road from here). I am SO buying that issue ;-).

  7. #7 Jim Thomerson
    May 29, 2008

    The Endangered Species Act uses species rather broadly. A distinctly different population of a biparental organism can be called a species for purposes of the act. I think this is the case for the Polar Bear, which may or may not be a species, depending on species definitions.

    I like the biological species concept, with all its warts, because it leads to the generation of testable hypotheses. It is least useful when considering allopatric populations, which is when you need it most, I suppose.

  8. #8 Jud
    May 29, 2008

    bob koepp @#4 -

    What you say is logical, but doesn’t square with ID/Creationist belief. One sample from one Creationist website (there are literally thousands more examples):

    God made the kinds of plants at the beginning and made them to reproduce after their kind. There is diversity or variation within each kind, allowing for adaptation to environment, yet each kind remains the same kind. This agrees with what we see in nature today, but conflicts with evolution.

    If that were true, there would be no reason at all for one kind to be similar to any other kind. Only if evolution were true – if kinds were not created immutable, but instead changed from one kind to another via evolution – would we be presented with the messy continuum of life that makes line-drawing between species so difficult in the real world.

    The very same old argument about immutability of “kinds,” dressed up a bit, is presented as “micro-evolution occurs, but macro-evolution is impossible” by Intelligent Design writers. You need look no further than Behe’s “The Edge of Evolution,” published just last year, for an extended exposition of this mythical principle.

  9. #9 Karl
    May 29, 2008

    Some time ago (months) I questioned, on this blog, the concept of species. I got a lot of the same answers as here. I still question the concept as being completely artificial, a remnant of the biblical “kinds”. The primary reason for my position is ring species. For there to be any validity to the concept of species, it must be (it seems to me)a transitive relation: (A ss B and B ss C => A ss C). And for ring species this doesn’t hold.

  10. #10 joek
    May 29, 2008

    Isn’t pretty clear from anthropology that “species” is a phenomenon of the human perceptory apparatus? All cultures have a concept of “species”, of kinds of organism that are basically the “same”, and are ranked into a taxonomy of some sort (“flying things”, “things with feathers”, etc).

    It’s not a “cultural” thing, like Karl suggests, but like mountains in Wilkins post – they are things everyone sees, they are subjective representations of an external reality, and that representation has been evolved into the human mind — and probably everybody else with a sophisticated enough mind, as well.

  11. #11 bob koepp
    May 29, 2008

    Jud – I think you’re conflating the questions of whether there are sharp boundaries between species and whether species are mutable. There can be connections between the two issues, but they need to be clearly distinguished.

  12. #12 Jud
    May 29, 2008

    bob koepp wrote: Jud – I think you’re conflating the questions of whether there are sharp boundaries between species and whether species are mutable. There can be connections between the two issues, but they need to be clearly distinguished.

    I plead not guilty to the former (conflation), but I definitely am seeking to draw connections.

    That is why I said “If that [creation of separate immutable kinds] were true, there would be no reason at all for one kind to be similar to any other kind,” rather than saying there could be no similarity. The latter is logically false (that there could be no similar kinds) but what I actually said (there is no logical reason for similarity of kinds if one holds to creationism) is correct.

    Evolutionary theory provides the logical reason to expect what we actually find in nature – such similarity of kinds, or species, that it is sometimes difficult to tell where one leaves off and another begins.

  13. #13 leigh
    May 29, 2008

    It may help slightly in clarification to note that what are now called fuzzy sets were first defined in the context of separation of species in evolution.

  14. #14 Jim Thomerson
    May 29, 2008

    I don’t think there is a Procrustian solution to the question, “What are the criteria we use to recognize a group of organisms as a species?” I’m not sure a species of salmon and a species of marigold are the same thing, for example. Do we think the same about a group composed largely of self-fertilizing hermaphrodites compared to a similar group that is separate-sex biparental? I really don’t see any problem with ring species, but then I’ve never worked with one. One wonders if my opinion would change with that experience.

    My professional life has focused on identifying fish species. I think I have delt with real entities and I’m confident that the large majority of my identifications have been correct so far as one could know at the time. For example, When I made the first collection of an undescribed species, I identified it as its described sister species; best one could do at the time.

  15. #15 Jason Grossman
    May 29, 2008

    > If somebody asked me to write a short essay giving an overview
    > of my favourite topic, the nature of species, I doubt that I could.

    I have the same problem. That’s why I don’t like teaching the topics I specialise in. (Despite that, I am currently writing a short essay giving an overview of my favourite topic. But it keeps coming out very technical.)

    another obscure Australian philosopher

  16. #16 RBH
    May 29, 2008

    …and anyway, species were well described and identified long before genetics was developed, some two centuries before. So they must at least be things that can be observed in the absence of theory. Of course, some species are harder to identify than others, requiring techniques that are recent, but that still doesn’t make species theoretical objects.

    This brings me to my third alternative: species aren’t theoretical objects at all; they are objects that have phenomenal salience. That is, we do not define species, we see them.

    Two centuries ago, for all practical purposes one could actually see (most) species — they were big things like moles and mice and moose that are obviously differentiated. Hence the notion of “species” was based on the phenomenal salience of which you write: Any dumb fool can tell that a mouse is different from a moose. And “species” may well be an appropriate unit of analysis for critters like that.

    For other sorts of critters — say those pesky microbes (to maintain the alliteration) — it may not be an appropriate unit of analysis. What law of science says the units of analysis for big critters have to be same as for little bitty critters?

    Put another way, is biology (descriptively and/or theoretically) the same discipline whether one focuses on critters characterized mainly by vertical genetic lineages and sexual reproduction (most big critters) and critters characterized by a mix of vertical and horizontal genetic transmission yielding networks rather than nice Markov branching process lineages? Should we use the same unit of analysis for both? If yes, why?

  17. #17 John S. Wilkins
    May 29, 2008

    That’s a good question. Here is my answer:

    “Seeing” is a relative sort of thing. It is dependent highly upon the kinds of techniques we use to see with. Linnaeus forbade the use of microscopes, but now we routinely use them for species description (I watched a guy do polychaete taxonomy with a microscope because the buggers are too small even for a magnifying glass). As we get new assay techniques, we get new phenomena.

    Microbial taxonomy has always been a mixture of morphology of both cell and colony, along with the sorts of culturing techniques, genetic assays, and so on that we now have. Each new development in technique, such as staining techniques in vitro or in vivo gives us phenomenally salient clustering. Why not call these species? The only reason is that we have a prior theoretical explanation that we seek to make universal. Why would we do that? The answer has more to do with scientific interdisciplinary politics than we might like to admit.

    Mayr’s and Dobzhansky’s species concept (for Mayr did not invent it, and tried to suggest that he made Dobie’s definition complete, when all he did was apply it, IMO) never properly applied to plants, so are we to say that species only exist in animals? What other restrictions must be made? What about saying that although an entire clade of lizards is well differentiated, as some are asexual, some taxa in that clade are not species? It gets close to a reductio very rapidly.

    So I reiterate something that you may have missed, based on how you express yourself in the final sentence: species are not units of analysis. They are units, or objects, of observation. They are real enough things, that call for a plurality of explanatory accounts, depending on the actual processes by which they came to be.

  18. #18 Christopher Taylor
    May 30, 2008

    I like the mountain analogy.

    Growing up in New Zealand, there was a kind of seaweed you’d find at the beach called Neptune’s necklace (I don’t know how widespread it is worldwide). Neptune’s necklace is constructed of a series of water-filled bobbles, very popular with children because if you pinch them off in the right way they can be converted into water pistols. I’ve always imagined species (at least over time) as like the bobbles of Neptune’s necklace – each separate one is an individual unit, but they’re all interconnected and any one merges into the next.

  19. #19 RBH
    May 30, 2008

    So I reiterate something that you may have missed, based on how you express yourself in the final sentence: species are not units of analysis. They are units, or objects, of observation. They are real enough things, that call for a plurality of explanatory accounts, depending on the actual processes by which they came to be.

    You’re right: I did miss (or misread) that. The question in my last paragraph grabbed me and sent me off without thinking about what you actually wrote.

  20. #20 Chris Rowan
    May 30, 2008

    I also like the mountain analogy (well, I would!) – although of course, geologists don’t concern themselves with individual mountains very much (except in the case of isolated volcanoes) – we’re more interested in the aggregate properties of whole ranges.

  21. #21 KeithB
    May 30, 2008

    Maybe species is much like the idea of the limit in calculus.

    You can approach it on each side as arbitrarily close as you want, but you can never exactly land on it.

  22. #22 Carl Cox
    May 31, 2008

    Species as seen in the fossil record seem to be greatly different from species seen today, where the difference is based upon the ability to interbreed. Fossil record species are assumed to be made by macroevolution, while most current species are made by microevolution. Thus the term, species, conflates two possibly different ideas. The concept of species as discussed by this article would seem to take into account the possible different processes for the two types of speciation. Currently it is not possible to use accepted terminology to even discuss the difference between micro and macroevolution. I would hope for some definition of terms that would separate the object, species, from the method of getting there, speciation (macro or microevolution).

  23. #23 John S. Wilkins
    May 31, 2008

    By saying something like “species are made by microevolution” it is clear that you have swallowed the creationist Koolaid. Microevolution is by definition evolution below the species level. Macroevolution is evolution at (i.e., generating new species) or above the species level. That’s the technical definition.

    There is a problem of species identification for fossil taxa – that derives from the fact that very little information is preserved in fossilisation, and so we may be lumping more than one species into a single species because the evidence that separates them is not preserved. Likewise we may be splitting single species into several for the same reason. This is why paleontology has its own “definition” of species. Of course the species at the time were species the same ways species are now.

  24. #24 Krubozumo Nyankoye
    May 31, 2008

    Although I have no qualification to enter the discussion concerning the term species, and I find it very interesting, I do take small exception to the analogy to the term “mountain” in geology, because frankly, to the best of my knowledge, the term mountain, is not geological sensu strictu.

    It does not have any clear usefulness in geological discourse other than to refer to a uniformly recognized entity of geography. That is to say, one might refer to the volcanics of Mt. Etna or St. Helens.

    Perhaps a better analogy would be to rock or mineral both of which are terms used in a geological context but with similar problems of “fuzziness” to the term species.

    If I refer to “olivine” as a mineral I can observe in a thin section microscopically and identify by its optical properties, I cannot tell you specifically whether it is fosterite or fayelite. Similarly, of a hand full of igneous rock samples, without doing detailed point counts on minerals in thin section, I could not reliably claim they were gabbros or granodiorites unless there was some telling marker that could be seen in the loupe.

    The spectrum of classification of things is continuous, analog, not digital. We require a digital viewpoint to be able to construct classifications. They are useful in so far as they provide a general guide to recognizing what you see in the real world. They are not the real world. Get used to it.

    Science is not perfect, nor does it profess to be. But it works a lot better than anything else.

    Cheers

  25. #25 Dan Styer
    May 31, 2008

    My thoughts on the species concept come from my background in microbiology and botany, and from my personal life:

    (1) If a species is defined as “an interbreeding population”, how do you classify asexual organisms, like many microbes?

    (2) If a species is defined as “an interbreeding population”, then my wife and I (who have done no breeding outside our marriage) constitute a species.

    (3) Ring species have already been mentioned, so I won’t bring them up again.

    (4) A common occurrence in botany: Sometimes the organisms in nature break down into readily identifiable species — no one ever confuses round-lobed hepatica and sharp-lobed hepatica. Other times they don’t — the hawthorns (genus Crataegus) are notoriously confusing, with interbreeding and hybridization and species that merge into each other. The USDA PLANTS database lists 173 species of Crataegus, but other authorities give different figures.

    (5) We classify species according to what we perceive about them, and our senses have limitations. For example, scent is very important to flowers and to pollinators, but humans have a very poor sense of scent. Two flowers that look the same but smell different might well be reproductively isolated, but we’d know it only after the most intense research. Even more so if two flowers differed in their appearance in the ultraviolet, which bees can see but we can’t, or in the light-polarization properties of their petals.

    My conclusion is that nature is what nature is. Science is what helps us understand nature. Sometimes the species concept is useful, other times it’s not.

  26. #26 DiscoveredJoys
    May 31, 2008

    In the book “Metaphors We Live By” by Lakoff and Johnson they suggest that many concepts are expressed as metaphors of more basic experiential sensations. They say things like “Understanding our experiences in terms of objects and substances allows us to pick out parts of our experience and treat them as discrete entities or substances of a uniform kind”. In this case “species” is a metaphor for the more basic concept of “container”.

    The species container is an artificial boundary to help us think about the contents in discrete terms – even though the organisms assigned to the container may not fit neatly into our imposed categories.

    I’m sure that science could define “species” with exquisite accuracy – but we would then need fresh container terms for organisms (e.g. plants, microbes, viruses) which don’t map neatly into the “species” definition. The alternative is that we accept that “species” and other classification terms work well enough for our specific purposes, but we have to remain conscious that while a bunch of organisms may be metaphorically bounded, the boundary itself may be permeable.

  27. #27 Allen MacNeill
    May 31, 2008

    John Wilkins asked (in #17):

    “…so are we to say that species only exist in animals?”

    In a word, yes. I have pointed out elsewhere that the vast majority of people who have attempted to formulate monological definitions of “species” are people who have spent most of their lives studying animals (to be specific, members of the kingdom Animalia). Darwin, Dobzhansky, and Mayr (not to mention Gould) provide paradigmatic examples: Darwin was the world’s foremost expert on barnacles (Cirripedia), Dozhansky concentrated on Drosophila, Mayr studied birds, and Gould fossil snails.

    For reasons I can’t get into in this post, animals are peculiar. Their genetics, reproductive biology, and development all make hybridization problematic, and so evolutionary biologists (most of whom have concentrated on animals) have long been tempted to locate the boundary between species using reproductive isolation.

    But, as I have pointed out in a post at my blog (http://evolutionlist.blogspot.com/2006/03/origin-of-specious.html), the kinds of reproductive isolation observed among animals is not characteristic of other taxonomic groups, including the other eukaryotes. Furthermore, as Darwin himself pointed out, sterility is problematic as a criterion for taxonomic exclusion or inclusion. Even among animals, sterility between individuals supposedly members of the same “species” is often as extreme as between members of different “species”, and hybridization between members of different “species” (and, in all but animals, even higher taxa) is surprisingly common. And, as Lynn Margulis has pointed out, major evolutionary shifts have occurred as the result of “hybridization” (i.e. endosymbiosis) between totally unrelated groups of organisms.

    Personally, I believe that the obsession with “species” ultimately goes back to Platonic “ideal forms”. It is therefore doubly ironic that Ernst Mayr should be recognized as the most vigorous opponent of Platonic typological thinking, yet his “biological species concept” is, in practice, as typological as anything Plato advocated.

  28. #28 Torbj�rn Larsson, OM
    May 31, 2008

    How he manages to get up on a topic like that amazes me. It took me a good five years.

    Um, because of good teachers, like some obscure Australian philosopher?

    Proper classification is essential for designating the endangered list.

    Both making it proper and then using it. When Poor Taxonomic Practice takes some F****ing Liberties! things goes bad:

    [...] Bortolus presents the results of a paper survey of 80 ecological papers published from 2005 to 2007 in ten top-ranked peer-reviewed ecology journals. [...] Fully a third of the papers surveyed gave no authority whatsoever for the identity of the species surveyed! [...] As is de rigeur in this kind of discussion, Bortolus gives us examples of the kind of errors that can result from poor taxonomic practice. Some errors are fairly innocuous, but others can have fairly serious consequences. There’s the case of a restoration programme in San Francisco that included the propagation and replanting of the native littoral grass Spartina foliosa. Unfortunately, the actual specimens propagated were not S. foliosa, but the non-native S. densiflora, and as a result of the programme S. densiflora was transformed from a minor adventive to a significant invasive. There’s the case of three morphologically similar but ecologically distinct Mytilus mussel species, the decline of one of which due to the invasive spread of another went unnoticed for many years. There’s the case of a failure to distinguish Anopheles mosquito species in Burma resulting in the long-term targeting of a non-malaria-carrying species by control programmes instead of the actual malaria vector. Bad taxonomy does matter.

    @ leigh & Karl:

    It may help slightly in clarification to note that what are now called fuzzy sets were first defined in the context of separation of species in evolution.

    I didn’t know that, but recently a commenter on PT (IIRC Frank J), noted that fuzzy sets is a valid model of species. Some formulations of fuzzy sets can be transitive, at least in a fuzzy way. But other fuzzy sets can model Poincaré’s paradox on indistinguishability – in physics you can see for quantities A = B, B = C, but A ≠ C. [Note: I haven't read this thoroughly, so I could be mistaken about the status of the paradox. Here is a paper that claims fuzzy sets don't always resolve such paradoxes. Also, the related history of fuzzy sets doesn't seem to bear out the above claim of biology as the first specific application.]

    Biological species membership could be analogous to such quantities. For example, horses may give offspring with donkeys and zebras, but possibly donkeys don’t give offspring with zebras.

  29. #29 Torbj�rn Larsson, OM
    May 31, 2008

    Biology, like most sciences, has a need for units of measurement. And like most sciences those units need to be grounded in the real world. So what species, the “rank” of biology that it is agreed on most sides is the most or only natural one in the Linnean hierarchy, are determines many measures of biology in fields from genetics to ecology. If, as a significant number of specialists think, the rank is a mere convention, then those measures become arbitrary and meaningless.

    So, what sort of “unit” might a species be?

    For me as a physicist this is a conflation of concepts. Units of measurement applies to observations, those observations made on systems that can contain more or less identifiable (by such observation) objects. Such units are mere conventions, and are neither arbitrary nor meaningless.

    If objects can be distinguished, in a natural way as you suggest (“those units need to be grounded in the real world”), they are also neither arbitrary nor meaningless. But they will appear differently depending on context. Black holes as we prefer to observe in our perception of an AdS space are AFAIU thermal radiation in the dual CFT space.

    They are natural objects, not mere conveniences, but they are not derived from explanations, but rather they call for them…

    I assume that this means that they call for an explanation in the sense that mountains does, regards the relation between theories and nature.

    As you have described it, in as much as some populations can be identified with a biological species concept, the later is useful of course, the same goes for paleontology et cetera. In other cases they may be convenient symbols that we use to describe the results of our overactive pattern detector, in the same way that function isn’t the same as apparent design.

    If that is so, my conclusion would be that we should try to accept the useful concepts as suggested by cladistics et cetera, and try to abandon the remainders. And the useful concepts will evolve. For example, but you know this, to establish phylogeny in bacterias it may be easier to identify ecological populations:

    �What is really new about our approach is that we were able to combine both molecular data (DNA sequences) with ecological data in a single mathematical framework,� said Alm. �This allowed us to solve the inverse problem of taking samples of organisms from different environments and figuring out their underlying habitats. In essence, we modeled the evolution of a microbe�s lifestyle over millions of years.�

    One splendid example of the difficulty of applying the term �species� to a single-celled creature: 17 of those 25 populations are called V. splendidus, a name that was previously assigned to them based on classical taxonomic techniques. Alm and Polz can see now that V. splendidus has differentiated into several ecological populations.

  30. #30 leigh
    May 31, 2008

    1) For species, as elsewhere, it’s important to distinguish the ontic from the epistemic.
    2) A perhaps general concept, more comfortable to ecologists than to geneticists: “A species is a lineage (or a closely related set of lineages) which occupies an adaptive zone . . . different from that of any other lineage in its range and which evolves separately from all lineages outside its range.” (Taxon 25:233)

  31. #31 John S. Wilkins
    June 1, 2008

    Alan McNeil wrote:

    “Personally, I believe that the obsession with “species” ultimately goes back to Platonic “ideal forms”.”

    That is the Standard View, yes, but it is deeply false. The natural use of “species” by John Ray, Caspar Bauhin and others in the first instance had nothing whatsoever to do with logical or philosophical uses of the term. It was simply a vernacular term in Latin, akin to “kind” or “sort” in English (something Locke pointed out for the logical species in his Essay.

    In fact neither Plato nor Aristotle had much to do with natural species concepts. It was merely the use of ordinary language for a new concept that arose in the act of studying living things (initially, plants, for those who think only animals have real species). The first time either Plato or Aristotle make an entrance is when Whewell and Mill start to discuss natural kinds in connection to natural species, well after the notion had become universally accepted by naturalists.

  32. #32 Carl Cox
    June 1, 2008

    As Eldredge and Gould pointed out, a species usually remains in stasis from it’s first indentification to the time it dissapears from the fossil record. I have seen observations from the biological community that stasis is the same as we currently experience, in that there can be variation in the fossil record just as we see around us today. Most changes in current species are small, one or at most a very few DNA bases, even though some have fairly significant effect.

    With the sequencing of chimp and homo genomes, comparison has been made of the two. In three separate comparisons, one between genes that have changed as reported in Nature for Sept 2006, one focusing most on control sections reported in Nature for Sept 2007, and a study of genes affecting the brain comparing macaque and homo by HHMI reported in 2004, it can be seen that there are major changes in about 1% of the genes/control sections of the genome. The HHMI study noted that over 1000 bases are changed in the speciation, and looking at the changes reported in the other studies that appears to be about right.

    The recent studies have given us major improvements in what is known about speciation. They provide information of the possibility that microevolution – the changes seen in genomes currently that sometimes are labeled species because of reproductive isolation – is an entirely different process than macroevolution, which is the kind of change seen in fossil speciation. This has nothing to do with creationism or ID, as it is based entirely current science. But the current definitions of speciation, which include small changes leading to reproductive isolation and major changes as seen in the fossil record, conflate two possibly different processes. I would like the definitions of speciation to at least facilitate a discussion of those processes.

  33. #33 andrew kelman
    June 1, 2008

    Fuzzy or subjective explanations for species are not satisfactory since they have no expalanatory power in the real world where the reality of species underpins paleontology, at the very least. The fossil record does not show fuzzy or intergrading species (in general)

    It might be more fruitful to look for behavioural or genetic mechanisms that arose simultaneously with sexual reproduction that create a positive reinforcement of species
    as the possible range of mates for any individual.

  34. #34 Torbj�rn Larsson, OM
    June 1, 2008

    Most changes in current species are small, one or at most a very few DNA bases, even though some have fairly significant effect.

    AFAIU that depends on what happens to a population, for example bottlenecks or conversely large effective size, et cetera. John Hawks et al claims that humans are currently under accelerated selection due to increased effective population size. They find, in the part of the genome they looked at, roughly 2000 – 3000 SNPs (depending on the location of the sample) being driven by selective sweeps. AFAIU the number of genes that are selected for is about 1/100 of that.

    They derive a rate of selective fixation of 30 variants/10 generations, or 3 changes every 20 years or so. This rate is a 100 fold increase compared to around 100 000 years ago. So that would make historical fixation rate rate 1 change every 1000 years. Hmm. Given 1000, I assume mostly adaptive, fixations between species that means a possibility for new species every 10^6 years, even without adding changes in selective pressures during speciation, so I’ll say it is consistent.

    Well, I guess I don’t see any need for supposing the changes seen are different processes then. But such research drives home that there are periods of relative stasis and periods without depending on changes in population size and, I assume, selective pressures during speciation.

  35. #35 John S. Wilkins
    June 1, 2008

    Fuzzy or subjective explanations for species are not satisfactory since they have no expalanatory power in the real world where the reality of species underpins paleontology, at the very least. The fossil record does not show fuzzy or intergrading species (in general)

    Well if the deposition rates are continuous enough, that’s exactly what it shows, and examples of this have been known since the early 19th century. Even Gould and Eldredge give an example in their classic paper.

    Paleontology uses the most subjective definition or criteria for species of all biology. All they have are morphological characters and the stratigraphy, so from that they identify species as best they can. But we know from modern experience that morphology is not a good guide to species identification (Darwin gives the case of an Andean rabbit Owen identified as two species when they were two morphs of the same species, in the Journal of Researches), so at best paleospecies are merely a rough guide to species in the past.

  36. #36 Ian
    June 2, 2008

    “A while back I wrote on microbial species, which became a paper in History and Philosophy of the Life Sciences”

    So when (where?!) do us non-professionals get to read it?!

  37. #37 Carl Cox
    June 2, 2008

    Well if the deposition rates are continuous enough, that’s exactly what it shows, and examples of this have been known since the early 19th century. Even Gould and Eldredge give an example in their classic paper.

    These cases are rare, as Gould carefully points out, and some of the cases which I have been able to examine are explained by other than continuous change, such as hybridation, or a small change in hormone wash during early growth as in the cichlids.

    Paleontology uses the most subjective definition or criteria for species of all biology. All they have are morphological characters and the stratigraphy, so from that they identify species as best they can. But we know from modern experience that morphology is not a good guide to species identification.

    I thought the idea of this subject was to explore species definitions. Which is a better definition: one that takes into account major DNA driven morphological changes as opposed to very limited DNA changes, which could be different processes, or one that conflates the two? Perhaps what we see in the current biosphere may be just variation that can isolate breeding groups. That needs a name, but why use the same name for the major morphological change as for a minor change that interupts only reproduction?

  38. #38 Karl
    June 2, 2008

    Being a non-scientist, non-PhD, I am not familiar with and do not understand a lot of the previous discussion. BUT, I want to get my, additional, two cents in. Some time ago, on one of John’s threads about species I asked why St.Bernards and Chihuahuas are not separate species – since they cannot (physically) interbreed. John said it is because if you put all types of dogs on an island for a while you would end up with a collection of medium sized dogs that could all interbreed. It seems, further, that that is the same thing as is the case for ring species. In both cases, if all the intermediates die out, then (THEN) the groups at the end would be separate species. But until then they should be considered to be sub-species or families (or something). Further example: if all “species” of Homo still existed, including all the ones that are undiscovered, I think that they should all be considered the same species. After all, isn’t there a theory that H.Sapiens and H.Neanderthalensis could interbreed? There were probably individuals with morphologies between the two – they just haven’t been found.

  39. #39 John A. Davison
    June 3, 2008

    Theodosius Dobzhansky proposed a perfecty valid and testable definition of species. Two organisms are the same species if their sexually produced progeny are fertile. This is a physiological definition of species which must be tested whether or not the two forms naturally breed or not. That criterion is rarely implemented. We know from zoo observations, notably wth bears, that many organisms once thought to be separate species are actually one. The physiologoal criterion would most certainly reduce the number of forms considered to be separate species. In any event, true species are genetically isolated from one another and, as far as we are able to tell, are unable to undergo further evolution.

    It is my conviction that no organism reproducing by obligatory sexual means is capable of organic evolution beyond the level of variety or subspecies. Sexual reproduction is conservative and anti-evolutionary. I also believe that the contemporary biota is the terminal product of a creative evolution no longer in progress. Today we witness only extinction with no verified replacements.

    “A past evolution is undeniable, a present evolution undemonstrable.”

    john.a.davison.free.fr/

  40. #40 John S. Wilkins
    June 3, 2008

    John, despite your obvious creationism, I will answer your point here. If you think Dobie’s definition was the universal definition of species, then you are unable to assign to species most of life (which is the point of my comment in the Scientific American article). Plants often hybridise. Lizards often hybridise. Birds often hybridise. Even tigers and lions will (fertilely) hybridise. Basically, Dobie’s definition only works if, like Coyne and Orr, you add the arbitrary qualifier “usually”. This is not some claim of evolution; it’s observable now.

    As to your final comment, you are entitled to believe anything you like, but you aren’t entitled to your own facts. New species have been observed in the lab and the field.

  41. #41 John A. Davison
    June 3, 2008

    John

    New species cannot be verified by field observations, only experimentally. “Dobie” is also the Darwinian who proved experimentally that Drosophila melanogaster cannot be transformed into even a new member of the same genus. The real mystery is how he remained a Darwinian.

    As for my “obvious creationism” I am a creationist exactly as was Albert Einstein, with no room for a personal God.

    Sine you are so sure that current creative evolution is in progress, please document that assertion with experimentally verified examples. No one else has. Just think, you could become famous by being the first to prove that Julian Huxley, Robert Broom and John A. Davison were all dead wrong. I’ll leave a light on for you.

    Good luck.

    john.a.davison.free.fr/

    “A past evolution is undeniable, a present evolution undemonstrable.”

  42. #42 VMartin
    June 3, 2008

    I would say more and more voices would support professor John Davison opinion that evolution is over and sex – once established – prohibit any further evolution. No lesser scientist than Wilson published in 2006 his “Rethinking the Theoretical Foundation of Sociobiology” where he entirely dismissed kin selection as plausible explanation of eusociality. He mentioned meiosis (I suppose in sexualy reprodcing animals) as stabilizing factor. Professor Davison’s concept regarding meiosis refers to saltationism. What a coincidence!

    There is no need to emphasize the role of natural selection in evolutionary processes. It plays only conservative role. Btw. no one neodarwinist know on which level natural selection operates. Some say it is genes, some say (like Wilson) it is groups. “Natural selection” thus seem to be some mystic power no one can really apprehend.

  43. #43 woodsong
    June 3, 2008

    Torbjorn:

    “For example, horses may give offspring with donkeys and zebras, but possibly donkeys don’t give offspring with zebras.”

    Ah, but they do!
    http://en.wikipedia.org/wiki/Zeedonk

    Some other interesting hybridization examples (also from Wikipedia):

    Cama (male Dromedary camel & female llama, bred by artificial insemination), Wholphin (False killer whale & bottlenose dolphin), Liger (male lion & female tiger), Tigon (female lion & male tiger), grizzly-polar bear hybrid, Hybrid Iguana (marine iguana & lans iguana), etc.

    For more:
    http://en.wikipedia.org/wiki/Hybrid_%28biology%29#Interspecific_hybrids

    This site also mentions some examples of animal species thought to be a result of hybridization (Lonicera fly, Pomarine skua).

    John A. Davison:

    “Sine you are so sure that current creative evolution is in progress, please document that assertion with experimentally verified examples. No one else has.”

    Raphanobrassica, anyone?
    http://en.wikipedia.org/wiki/Raphanobrassica

    Or a few others:
    http://en.wikipedia.org/wiki/Category:Recent_speciation_events

    http://en.wikipedia.org/wiki/Allopatric_speciation

    http://en.wikipedia.org/wiki/Sympatric_speciation

    That didn’t take long….

  44. #44 Jim Thomerson
    June 3, 2008

    I am in partial, limited agreement with John Davidson. In the group of fishes I am most familiar with, I think the allopatric speciation model has considerable explanatory power. The idea that speciation occurs after physical (usually geographic) separation of a population into two or more. Suppose this separation has occurred. The results could be:

    1. Extinction of one or more populations.
    2. Nothing much, the populations get back together and one might or might not suspect that they had ever been separated.
    3. Speciation.
    4. etc.

    I have thought about this a good bit, and discussed it with various colleagues. My conclusion is, that were I to be in the midst of a speciation event in the field, I would not be able to recognize it because there are various possible outcomes as listed above. So I tend to look at nature from the point of view of seeing the results of past speciation events. Looking at similar, but maybe not the same, populations and asking the question, “Are these populations the results of a speciation event?”

    I’ve done a lot of playing with hybrids, doing Dobzhansky’s hybridization test. In one case, I was able to readily breed homospecific pairs of two species (jumping ahead of the story) under the same set of aquarium conditions, but had no success with heterospecific pairs. Found out later that breeding behavior in nature was strikingly different and the karyotypes were different enough that a viable hybrid was unlikely.

    In another case, I was hybridizing two species (one with 40, the other with 48 chromosomes) to see if they would; and, if so, what do the hybrids look like. As it turns out I had no trouble making hybrids, backcrosses, etc. However when these two species occur together (only 19 known localities in a huge overlapping range) there are very few hybrids and little introgression.

    So, if you can happily reproduce the two species under the same conditions in the lab, bur they will not hybridize, you have two species, fide Dobzhansky. On the other hand, if they hybridize freely in the lab, maybe they are not two species, but you do not know unless you know what they do when in contact in nature. An how do you test that if they are distributed alloptrically in nature, as they should be after a recent speciation event?

    Lack of hybridization (or various strange outcomes, all sterile male F1′s. for example) supports two species. Full hybridization in the lab suggests a single species, but that is not definitive, and may not be the case in nature.

  45. #45 jeff
    June 3, 2008

    There is no need to emphasize the role of natural selection in evolutionary processes. It plays only conservative role. Btw. no one neodarwinist know on which level natural selection operates. Some say it is genes, some say (like Wilson) it is groups. “Natural selection” thus seem to be some mystic power no one can really apprehend.

    Until it happens to you. And how do you explain convergent evolution without natural selection? A bit more than a conservative role there, it seems.

  46. #46 John A. Davison
    June 3, 2008

    As near as can tell there are no recent creative evolutionary events. I have repeatedly requested examples of newly evolved species with their source and have yet to receive a convincing example. Wilkins can say all day long that it is going on but the proof is in the pudding. It cannot be assumed but must be established by demonstrating that the progeny is sterile when back crossed to the parent. I don’t even know of a case in which the parent is even known for a new true species and neither does anyone else. It is my conviction that no sexual organism is competent to produce a new species according to the criteria establshed by Dobzhansky.

    There is no question in my mind that creative, ascending speciation is a phenomenon of the distant past. Phylogeny, exactly like ontogeny, has been the history of the loss of potential until today all we see is extinction. There is no evidence that a single recently extinct species has been replaced. This is especially significant during a period in which the environment has been drastically altered due to the ravages of modern civilization. We are living in the terminal era of a planned evolutionary scenario, one which will end with our own extinction along with most of our fellow creatures. Homo sapiens, the final product of a planned evolution may very well prove to be the species with the shortest life span.

    This why I repeat -

    “A past evolution is undeniable, a present evolution undmeonstrable.”

  47. #47 John S. Wilkins
    June 3, 2008

    John, three things:

    1. Why did you say on Panda’s Thumb that you were banned here? You never have been here.

    2. If you want to stay unbanned, don’t continue to argue creationism. This blog, which is like my living room, is for I and others to discuss things of interest. It’s not a forum for preaching. If you want to point out, with citations, evidence that you think is problematic for evolution, I will allow it, but preaching is right out in this coffee klatsch.

    3. Dobzhansky himself showed speciation in the lab, inadvertently, for Drosophila:

    Dobzhansky, T. 1973. Species of Drosophila: New Excitement in an Old Field. Science 177:664-669

    As to why it can’t be observed in the field, that makes no sense at all. Botanists have observed speciation frequently (made easier because their events are often polyploidies). Lizard specialists (I can’t recall their title) observe speciation in anole lizards and various others that are in statu nascendi.

    It seems to me that you have defined away this evidence. Because it happens at rates too slow for humans to have had much chance to see the outcomes, mostly, you are inferring that we never see it. But since we often won’t know until after the fact that it actually was speciation in process we saw, you get a free pass. However, that isn’t how science works.

  48. #48 Joh nA. Davison
    June 3, 2008

    John

    I most certainly was at Panda’s Thumb just as I once was at After the Bar Closes, ARN, EvC, RichardDawkins.net and briefly at Pharyngula. I recommend you read my “Why Banishment” thread where I review my history on internet blogs in some detail.

    I also reject gradual evolution. It is a myth. All real creative evoltion was instantaneous as was the creation of all the taxonomic categories. The entire Darwinian edifice is a disaster without a shred of tangible support. It was dreamed up out of thin air by a pair of Victorian naturalists, one of whom, Alfred Russel Wallace, had the good sense to reject it entirely later in life.

    Thanks for allowing me this opportunity to respond.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  49. #49 John S. Wilkins
    June 3, 2008

    But you never have been banned here, so why did you say that? If you said it deliberately in the knowledge it was false, then that was a lie. I trust you will return to Panda’s Thumb and correct it.

    Wallace never abandoned gradual evolution. He decided it could not account for human cognitive faculties, which is rather different. I suspect you have never read Wallace. I have (in first editions no less – the joys of being a PhD student at the right place and time).

    Finally, you have made your slogan comment twice now. Do not make it again – we get the idea…

  50. #50 VMartin
    June 4, 2008


    Until it happens to you. And how do you explain convergent evolution without natural selection? A bit more than a conservative role there, it seems.

    “Good” irony.

    two points:
    1) Hamilton/Dawkins idea of “kin selection” or “inclussive fitness” or “selfish gene” has been totally dismissed by no lesser scientist than Wilson in his “Rethinking the Theoretical Foundation of Sociobiology”. Oddly enough the book “The Selfish gene” should be the most read and influential non-fiction book in the 20th century. Professor Dawkins himself wrote that idea of kin selection as applied to eusociality is “one of the most spectacular triumph of the theory”. It turned out to be wrong. One has to ask on which foundation now kin selection now stands.
    People were held in fallacy for almost 30 years. One should ask if it is not better to dismiss the whole concept of “natural selection” because the greatest neodarwinian thinkers of our time do not know on which level it really operates (individuals, groups, genes?) and instead spread ideas which contradicts each other calling neodarwinism “science”. This is very strange.

    2) Convergent evolution you asked me about: It is presumed that striking similarities between some marsupial and placental animals (sabretooth cats or wolfs) is due similar “niche”. John Davison claims it is due prescribed evolution. I agree with him. My argument is this: there are several polymorphic butterflies species where females of the same spieces “mimic” wing patterns of unrelated butterflies. But some of females of the same “mimicking” species do not mimic anything. Obviously the niche is almost identical and one has to be hard-core selectionist to see in these cases “different niche”, “adaptation” and “survival advantage of mimicry”. There is no place here discuss it into more details, I addressed the whole point of mimicry at other forums. Just a remark – the “niche” as the explanation of evolution is so elusive as the “natural selection” itself. It requires only belief, because no one can prove it.

  51. #51 John A. Davison
    June 4, 2008

    Martin

    Many thanks for your loyal support and incisive comments.

    John

    I can’t return to Panda’s Thumb, Pharyngula, After the Bar Closes, ARN, EVC, Uncommon Descent, RichardDawkins.net and many other weblogs since I have been banished from them because I am neither a Darwinian atheist nor a religious fanatic. Now tou are threatening me with the same if I simply repeat my signature convictions.

    Here is your opportunity to prove to the world that you are no different than Bill Dembski, David Springer, Wesley Elsberry, Richard Dawkins, P.Z. Myers or Percy over at EVC, whoever that is. By denying me voice you will firmly establish your insecurity just as they all have. That option is yours and yours alone. If you think you can control me with threats you are sadly mistaken.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  52. #52 John A. Davison
    June 4, 2008

    John

    I am very familiar with Alfred Russel Wallace. I have both his “Man’s Place In The Universe” and his last book. “The World Of Life: A Manifestation Of Creative Power, Directive Mind and Ultimate Purpose.” I will let others draw their own conclusions as to his posture with respect to organic evolution. He finally rejected the entire Darwinian paradigm in no uncertain terms.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  53. #53 John S. Wilkins
    June 4, 2008

    You mean this “Man’s Place in nature”?

    As Darwin solved the problem of the origin of organic species from other species, and thus enabled us to understand how the whole of the existing forms of life have been developed out of pre-existing forms, so astronomers hope to be able to solve the problem of the evolution of suns from some earlier stellar types, so as to be able, ultimately, to form some intelligible conception of how the whole stellar universe has come to be what it is. [p98]

    You mean this “World of Life”?

    IN the present volume I have attempted to summarise and complete my half-century of thought and work on the Darwinian theory of evolution. In several directions I have extended the scope and application of the theory, and have shown that it is capable of explaining many of the phenomena of living things hitherto thought to be beyond its range. [p1]

    Many people imagine, however, that Darwin’s theory proves that there are no such things as species ; but this is a complete misconception, though some biologists use language which seems to support it. To myself, and I believe to most naturalists, species are quite as real and quite as important as when they were held to be special creations. They are even more important, because they constitute the only definite, easily recognised, and easily defined entities which form the starting-point in all rational study of the vast complex of living things. They are now known to be not fixed and immutable as formerly supposed ; yet the great mass of them are stable within very narrow limits, while their changes of form are so slow, that it is only now, after fifty years of continuous search by countless acute observers, that we have been able to discover a very few cases in which a real change the actual production of new species appears to be going on before our eyes. The reader may therefore rest assured that there is no mystery in the word species, but that he may take it as meaning the same as kind, in regard to animals and plants in a state of nature, and that he will have no difficulty in following the various discussions and expositions in which this term is necessarily so prominent. The reason why species is the better term is because kind is used in two distinct senses that of species when we speak of kinds of deer, of squirrels, or of thrushes, but also that of a genus or a family when we speak of the deer, squirrel, or thrush kind, as meaning the whole group of these animals. If we used the word tribe instead of kind in this latter sense, all ambiguity would be avoided. [p11-12]

    The facts outlined in the present chapter, of abundant and ever-present variability with enormous rapidity of increase, furnish a sufficient reply to those ill-informed writers who still keep up the parrot-cry that the Darwinian theory is insufficient to explain the formation of new species by survival of the fittest.

    They also serve to rule out of court, as hopelessly inefficient, the modern theories of “mutation” and “Mendelism,” which depend upon such comparatively rare phenomena as “sports” and abnormalities, and are, therefore, ludicrously inadequate as substitutes for the Darwinian factors in the world-wide and ever-acting processes of the preservation and continuous adaptation of all living things. The phenomena upon which these theories are founded seem to me to be mere insignificant by-products of heredity, and to be essentially rather self-destructive than preservative. They form one of nature’s methods of getting rid of abnormal and injurious variations. The persistency of Mendelian characters is the very opposite of what is needed amid the ever-changing conditions of nature.

    It’s not enough to merely own the books, John. You also have to read them…

  54. #54 Thony C.
    June 4, 2008

    It’s not enough to merely own the books, John. You also have to read them…

    Posted by: John S. Wilkins | June 4, 2008 7:57 AM

    I thought they were there to cover the dirty patches on the wallpaper!

  55. #55 John S. Wilkins
    June 4, 2008

    I must, however, apologise for stating that John had said on Panda’s Thumb that he was banned here. John tried to say that, but the comment was not approved because it turns out he was indeed banned there. So he need only apologise to me, as I am the only one who saw that lie.

  56. #56 John A. Davison
    June 4, 2008

    John

    I don’t care for your tone but I will respond nevertheless.

    I presented the full title of “The World Of Life: A Manifestation OF Creative Power, Directive Mind And Ultimate Purpose.” Do you really believe that title can ever be reconciled with an evolution driven by chance and selection? I don’t. His statement that you have cited has no bearing on the only problem which is central to the mystery of organic evolution. Wallace, like myself and every one of my many sources, never denied the reality of evolution.

    The only issue that has ever been at stake is the MECHANISM by which evolution took (past tense) place. Natural selection never had anything to do with the emergence of any new life form and had very little to do with its subsequent modification. The vast majority of all organisms that ever existed remained unchanged from the moment of their instantaneous inception until the day of their final extinction. I believe that extinction was scheduled in advance just as was all evolutionary emergence. In the past there was a balance between creative evolution and extinction, a balance no longer in effect. We have reached the ultimate goal of a planned evolution which was the appearance of Homo sapiens, probably the youngest mammal on the face of the earth, emerging in his present final configuration a mere 150,00 years ago. Today we see only extinction without a single replacement having been produced for the thousands, perhaps millions, of species which have become extinct in historical times, largely due to the destruction of their habitats by man, a destruction which continues to this very day.

    Phylogeny exactly like ontogeny, has proven to be a goal directed, self-limiting process, a process no longer in effect. I don’t expect others to agree with my conclusions, however I am certainly not alone in my view of the great mysteries of ontogeny and phylogeny as the following will testify.

    “Neither in the one nor in the other is there room for chance.”
    Leo Berg, Nomogenesis page 134.

    “The struggle for existence and natural selection are not progressive agencies, but being, on the contrary, conservative, preserve the standard…. Evolution is in a great measure an unfolding of pre-existing rudiments.”
    Nomogenesis, page 406.

    “To insist, even with Olympian assurance, that life appeared quite by chance and evolved in this fashion, is an unsupported supposition which I believe to be wrong and not in accordance with the facts.”
    Pierre Grasse, Evolution Of Living Organisms, page 107.

    and finally from Robert Broom, who believed there was a Plan, a word he capitalized –

    “In the last work of Russel Wallace, published in 1910, three years before his death, he says ‘In the present work I recur to the subject after forty years of further reflection, and I now uphold the doctrine that not only man alone, but the whole World of Life, in almost all its varied manifestations, leads us to the same conclusion – that to afford any rational explanation of its phenomena, we require to postulate the continuous action of higher intelligences; and, further, that these have probably been working towards a single end, the development of intellectual, moral and spiritual beings.’”
    Robert Broom, Finding The Missing Link, page 105.

    My only qualification is that I do not believe it is necessary to assume a “continuous action.” All that is required is a goal-seeking mechanism, one which finally achieved its end.

    “A past evolution is undeniable, a present evolution undemonstrable.”

    Nomogenesis, page 406.

  57. #57 JohnA. Davison
    June 4, 2008

    John

    I dont get it. Why should I apologize to you? What have I done wrong? I hope you plan to present my latest rather lengthy response to your message #53. If you do I promise to go away as there will be no compelling reason to futher participate here.

  58. #58 John A. Davison
    June 4, 2008

    John

    I expect you to present my response to your message #53. If you fail to do so it will become a matter of permanent record both at “brainstorms” and on my weblog.

  59. #59 leigh
    June 4, 2008

    “Also, the related history of fuzzy sets doesn’t seem to bear out the above claim of biology as the first specific application.”
    The relevant paper appeared in a rather obscure book, Form and Strategy in Science (Gregg & Harris, ed., 1964), which had been making the rounds of publishers for several years. The concept is called ‘stochastic sets’ there and differs from Zadeh’s of 1965 by a constant of scaling.
    “These cases are rare, as Gould carefully points out, and some of the cases which I have been able to examine are explained by other than continuous change, such as hybridation, or a small change in hormone wash during early growth as in the cichlids.”
    All species transitions except some by polyploidy are very gradual at an ecological scale, as Gould carefully points out. A well-studied example is the origin of Homo sapiens.
    “Paleontology uses the most subjective definition or criteria for species of all biology. All they have are morphological characters and the stratigraphy, so from that they identify species as best they can.”
    A good example of the need to distinguish the ontic (what species are) from the epistemic (how we recognize them.) We paleontologists infer species boundaries by different criteria than we define them.
    “Theodosius Dobzhansky proposed a perfectly valid and testable definition of species. Two organisms are the same species if their sexually produced progeny are fertile.”
    He said no such thing, ever. Reproductive isolation, which he discussed at length, is a simple concept but not as simple as that.

  60. #60 John A. Davison
    June 4, 2008

    John

    You have until 8 PM EST to present my response to your message #53.

  61. #61 John S. Wilkins
    June 4, 2008

    First of all, as you must know having read Wallace, the earth is round. That means when it is light on your side of the globe, it is often dark on this side, which is when I mostly sleep. So setting deadlines like that is silly.

    Second, you said, and I quote:

    I am very familiar with Alfred Russel Wallace. I have both his “Man’s Place In The Universe” and his last book. “The World Of Life: A Manifestation Of Creative Power, Directive Mind and Ultimate Purpose.” I will let others draw their own conclusions as to his posture with respect to organic evolution. He finally rejected the entire Darwinian paradigm in no uncertain terms.

    The quotations show that not only did he not reject the Darwinian “paradigm”, he defended it in his last books. That he accepted a non-natural origin for mind is neither anti-Darwinian (as Gray also held that), nor relevant to his acceptance of Darwin’s theory. He went so far, as the quotations show, as to deny that the Mutationstheorie views that the early Mendelians put forward were in fact contrary to Darwin’s theory, and Castle, then Fisher and Sewall Wright alls howed this to be the case.

    Third, argument by book title indicates I was right about your having read, or at least understood, Wallace’s views. Berg’s and Grasse’s views do not confirm this interpretation, because, well, the author’s intentions trump those of people who are trying to use that author as evidence for their own views. Scientists are not historians of their science, and they use prior authors in all kinds of ways, but if you want to make a claim about what the author said, go to the author.

    Finally, when you tell a lie about someone, and you are shown to have done so, the polite thing is to apologise. You tried to say in a public forum that I had banned you here. This was a lie, and you knew it to be so. I know you have your martyr’s complex to feed, but an apology should be forthcoming anyway.

  62. #62 Jim Thomerson
    June 4, 2008

    So far as recent speciation events go, there is a discussion of several over at Talk Origins. To stay with the Allopatric Speciation Model, it is probably going to take a bit of time for the two separated populations to pick up enough genetic divergence to have speciated. Depending on circumstances, it could be many, many generations. Probably not something to be observed on a two-week field trip. So, one would reasonably think there would be few examples of allopatric speciation occuring within the short span of modern times. To think otherwise is not logical.

    The comment that the present rate of species extinction is much higher than the present rate of speciation is undoubtedly correct. We are in the midst of one of the great mass extinctions, I think.

    As far as animals are concerned, speciation events usually take, from an human perspective, a long period of time. However the origin of higher categories is practically instantaineous. How can this be?

    I think species exist in nature, and my function is to identify individuals of known species, and to RECOGNIZE, describe and name those previously unknown to science. When my colleagues and I name a new species, we are not creating the species in a biological sense, but rather recognizing a previously existing entity.

    On the other hand, higher categories are CREATED by fools like me. Been there, done that! Categories from Genus on up are human constructs to reflect how we interpet the differences and similarites among species to clarify their phylogenetic relationships. Creation of higher categories, even though we gripe about publication delays, is thus practically instaintaneous.

    About reproductive isolation, there is a large literature on premating and postmating isolation mechanisms. What happens in the lab may illuminate what happens in nature, but it is in nature that is important. Suppose we find two species coexisting in nature without a sign of hybridization. We bring them into the lab and they hybridize like it was going out of style. Hey, we still have two species.

  63. #63 Karl
    June 4, 2008

    “A past evolution is undeniable, a present evolution undemonstrable.”

    Posted by: John A. Davison
    ——————————————————–
    Take a look at http://www.talkorigins.org/faqs/comdesc/section5.html#speciations

    “Speciation of numerous plants, both angiosperms and ferns (such as hemp nettle, primrose, radish and cabbage, and various fern species) has been seen via hybridization and polyploidization since the early 20th century.”

    ” Many Drosophila speciation events have been extensively documented since the seventies. Speciation in Drosophila has occurred by spatial separation, by habitat specialization in the same location, by change in courtship behavior, by disruptive natural selection, and by bottlenecking populations (founder-flush experiments), among other mechanisms.”
    ” Several speciation events have also been seen in laboratory populations of houseflies, gall former flies, apple maggot flies, flour beetles, Nereis acuminata (a worm), mosquitoes, and various other insects. ”

    “Speciation has also been observed in mammals. Six instances of speciation in house mice on Madeira within the past 500 years have been the consequence of only geographic isolation, genetic drift, and chromosomal fusions.”
    —————————————————-
    John (Wilkins) I think you are wasting your time with this guy. I expect that he will deny that any of the above examples satisfy his criteria. He will say that there were not REALLY any NEW species created, only variations within species. He doesn’t really accept the definition of species, he’s talking about “kinds”. What he wants to see is a dog giving birth to a cat, or a canary, or something.

  64. #64 John S. Wilkins
    June 4, 2008

    I know I am. Davison is a well known ID creationist. He knows the literature cited (well, he knows the citations – given his inability to read Wallace I am betting he either hasn’t read or didn’t understand the papers) at the Talkorigins.org FAQ.My bet is he will now appeal to a “microevolutionary” explanation for the creationist definition of “microevolution” (that is, “it’s still a Drosophilid/fern/housefly”) to claim this isn’t real evolution at all. Goalposts need to be planted on iceskates for these guys.

  65. #65 John A. Davison
    June 4, 2008

    John

    What your sycophantic fans don’t know is that you published my response to your message #53 only after I threatened to expose you if you didn’t. You are no different than P.Z. Myers. Protectionist of the Darwinian fairy tale, you play fast and loose with reality to preserve the myth for as long as possible. By presenting my comments out of sequence you make it look as if I complained that you had not published my response after you had presented it which is a blatant lie. You are “prescribed,” ethical trash in the same vein as Wesley Elsberry and P.Z. Myers. None of you atheist zealots have ever published a word on the mythology you so feverishly preserve. Neither has Dawkins. He just thinks he has!

    You have also deliberately misrepresented Alfred Russel Wallace, making it look as if he was a lifelong Darwinian. Nothing could be further from the truth.

    For those who might want to know the truth about you and your tactics, they will find a full explanation on my weblog and elsewhere. Thanks for exposing yourself.

    I have never moved the goalposts set by Dobzhansky. I stand by my assertion that creative evolution is a phenomenon of the distant past. The examples cited are trivial subspecific dead ends none of which are incipient true species. The tests for hybrid sterility were not even attempted, let alone established. As far as can be firmly established there is not a single contemporary organism on the face of this earth that is capable of any fundamental progressive change. If such an event should occur, I can assure you that it would not be through sexual reproduction.
    Sexual (Mendelian) inheritance never had anything to do with speciation or the production of any of the higher taxonomic categories. With very few exceptions, all sexual forms were in the past and are still doomed to ultimate extinction.

    If you were a man you would publish this response in proper sequence. Consider that my test of your integrity because that is exactly what it is.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  66. #66 Karl
    June 5, 2008

    Since you are moderating comments, I will write this to you, a little bit off the current topic, and not for the comment list. I have written before about not being happy with the concept of species. My problem is illustrated by ring species and transitivity. As I said above, A ss B, B ss C => A ss C. So the ends of a chain of a ring, even though they are contiguous and don’t interbreed, must still be the same species. This also goes back to your explanation about big dogs and small dogs on an island. I maintain that you can only have new species when all of the intermediates between two groups have gone extinct. I think that I read that somewhere: you or Gould or ?. My conclusion therefore, unfortunately, sounds like a creationist’s, when there are only a series of small (microevolution) changes and all of the intermediates exist, no new “kinds” have been created. The difference for me is that I believe that it is clear that the difference between micro- and macro- evolution is just a matter of time or isolation. I just have a problem with defining when you have a new species.
    I suggest that you adopt PZ’s recently stated policy about comments – something about when a commentor gets too obstreporous, he gets banned. It gets tiresome wading through the same statements over and over. Otherwise, I’m a big fan of yours.

  67. #67 Karl
    June 5, 2008

    And, by the way; you used the “moving goalposts” analogy to describe that behavior. I was going to describe it as an example of the “No TRUE Scotsman” fallacy. I guess they’re really the same thing.

  68. #68 Brian English
    June 5, 2008

    Doesn’t Mr. Davison understand the concept of time zones? And the concept of a blog being run by the blogger and not the bloggee? I think he has issues.

  69. #69 John S. Wilkins
    June 5, 2008

    I tried explaining it in simple words, but he doesn’t seem to have worked it out. I think we can see why he’s been banned in so many places. He’s just an idiot.

  70. #70 Thony C.
    June 5, 2008

    J.A.D wrote:

    John

    What your sycophantic fans don’t know is that you published my response to your message #53 only after I threatened to expose you if you didn’t.

    I am confused, #53 is my not so funny comment on the true function of books that as far as I can see noboddy has responded to in anyway what so ever!

  71. #71 John S. Wilkins
    June 5, 2008

    Because Davison’s email address is not Trusted, his messages await my authorisation (when I am awake, that is), and so the numbers may have been revised when his comments were indeed approved.

    So far, none of his comments have been prevented from being posted. But as Brian pointed out, this is my sandpit, and if he pisses in it, he’ll be treated like Envall (that is, ignored hereafter).

  72. #72 woodsong
    June 5, 2008

    Heh. And JAD complains….

    I submitted a note June 3rd at around 2:00PM. I assumed timezone differences when it didn’t appear by the time I logged off (5:30PM), and didn’t worry about it.

    Now I come back and see that it’s still not here. Was there a problem with what I posted? Do you dislike Wikipedia links?

  73. #73 John A. Davison
    June 6, 2008

    So he is “just an idiot” is he?

    KMA and GFY

  74. #74 Jim Thomerson
    June 6, 2008

    I’m interested in how JAD understands subspecies. Subspecies is a formal taxonomic category. The first paper I was asked to review by an editor was a description of a new subspecies. Unfortunately the subspecies was based on a mathmatical mistake, and the paper never saw the light of day. I have only considered subspecies once. In this case there were two described subspecies and we elevated them both to full species status.

  75. #75 VMartin
    June 6, 2008

    I consider professor John Davison’s work on evolution “Evolutionary Manifesto” as the most inspiring anti-darwinian work available nowadays. I don’t see a reason why you are behaving as idiots. Are you so angry that somebody criticises your neodarwinian concept as pure fallacy? No wonder. Sometimes even Universities are full of fanatics unable to comprehend the light of wisdom. Giordano Bruno had his own experience in Oxford with pundits:


    …and if you do not believe this, go to Oxford and let them tell you the things that happened to the Nolan…
    .
    .
    .
    Let them tell you with what rudeness and discourtesy that pig [doctor] did proceed and with what patience and humanness did that other, who in fact showed himself to be a native of Naples.

    Giordano Bruno: LA CENA DE LE CENERI

  76. #76 John A.,Davison
    June 6, 2008

    John

    You use the same tactics as P.Z. Myers, a one way communication system that you and you alone control. You are both cowardly, insecure, “prescribed,” atheist blowhards neither of whom has ever published a word on the only matter that has ever been in question – the mechanism of a long ago terminated organic evolution. Thanks for granting me the opportunity to allow you to expose yourself in your own words.

  77. #77 VMartin
    June 7, 2008

    Karl wrote:


    John (Wilkins) I think you are wasting your time with this guy. I expect that he will deny that any of the above examples satisfy his criteria. He will say that there were not REALLY any NEW species created, only variations within species. He doesn’t really accept the definition of species, he’s talking about “kinds”. What he wants to see is a dog giving birth to a cat, or a canary, or something.

    But in fact your link does support such “saltationism”.
    I’ve checked the link on talkorigin you sent. Talkorigin as usually claims something without any relevant links. So I found this:

    http://www.holysmoke.org/cretins/speci.htm

    I don’t see how someone can use these examples as support for darwinian evolution or speciation. Karpchenko (1928) crossed radish with cabbage and obtained a hybrid.

    I would say such experiments prove more saltationism than any darwinian gradualism. A new species arise abruptly. No wonder we cannot find “missing link” if evolution proceeds this way. But these “species” are only abnormal indoor frankensteinian hybrids as some scientists written it down:

    However, these forms (Raphanobrassica) usually show such great irregularities in the distribution of their chromosomes, accompaniedwith prevalent infertility, that they very likely would not be able to compete successfully in nature and thereby survive.” (Marsh F.L.,”Variation and Fixity in Nature”, Pacific Press: Mountain View CA,
    1976, p57)

    I don’t really see how such hybrids should prove validity of neodarwinian fancy about gradual origin of species.

  78. #78 Jim Thomerson
    June 7, 2008

    Speciation as a result of hybridization seems to be common in plants. I think I read somewhere that some 25% of flowering plants are of hybrid origin. Basically, two species of plants produce hybrid offspring. The hybrid is infertile because the chromosomes of the two parent species are different enough that meiosis is not successful. Then polyploidy happens; there is/are hybrids who are tetraploid, ie with two sets of chromosomes. These tetraploid hybrids are interfertile and can produce fertile offspring. However, if they breed back to one of the parent species, they produce infertile triploids.

    There is also polyploidy within a species producing tetraploid individuals which cannot produce fertile offspring with diploid individuals. This is commonly promoted among commerical growers.

    So, this kind of speciation is essentially instantanious. It is, of course, no argument for the kind of long term allopatric speciation I think most important in animals. There is the situation where hybridization, in some fishes and lizards, results in all female species, but this is not widespread.

  79. #79 David Marjanovi?
    June 8, 2008

    LA CENA DE LE CENERI

    DEI CENERI.

    And when will you learn that the argument from authority is a logical fallacy? Culex molestans, the London Underground mosquito, is a 100-year-old species. Eat that. It doesn’t go away if you don’t know about it.

  80. #80 Bad
    June 10, 2008

    The Linnean hierarchy is the problem, not the solution, and if anything is to blame for creationist dissembling over whether “significant” evolutionary change can happen, it’s our incredibly confusing taxonomy. Mixing discrete ranking functions with grouping functions just doesn’t work very well.

    When you explain what a “species” is to a layperson, you end up conveying to them that species is both a rank in a quasi-discrete hierarchy AND a specific good group of animals. i.e. there are things called species, which are the lowest major “rank” in a heirarchy of life, and there are also specific groups of animals, defined by their characteristics and inter-breedability, that are particular species.

    But what happens when, thus armed, these people look at evolution? They see an ancient species “turning into” a modern species: a lateral move across the ranking system. In reality, the descendants of the ancient species are almost always properly within the “group” that the ancient species defined: every subsequent ancestor is a sub-variation of that species. And yet, many of those sub-variations have their own “species” name or even their own genus, or worse: which then implies lateral moves, rather than nested clades.

    Put it another way: every single modern land animal fits into the same “groups” that the very first land animal. Everything that made the first land-fish different from all other life continues to characterize all of its descendants. Amongst its descendants, there should never be a taxonomic “rank” any higher than it’s lowest “rank” (species). And yet, the Linnean system basically makes such confusion unavoidable.

    Unfortunately, the solution to all of this, a simple clade system with numbered nodes and so forth instead of ranks… is boring. :)

  81. #81 Jim Thomerson
    June 11, 2008

    Bad, I think you are wrong, but I am so bound up in the Linnean system that I cannot comprehend your argument well enough to refute it. There have been various numerical systems proposed. My problem with them is that I can remember names, but not strings of numbers. Also, if you wrote Rivulus as Ribulus, I probably would recognize the typo, but would not immediately understand that by 1846732 you ment 1856732. So it is more than boredom; and boredom is bad enough.

  82. #82 Jim Kidder
    June 15, 2008

    I addressed this question in the first chapter of my dissertation a decade back and also wondered what a species was. There is, of course the Dobzhansky/Mayr construct of the Biological Species Concept, which works very well for extant species but is not workable for fossil ones. I tend to lean more toward Simpson’s evolutionary species concept, because it seems to fit what I see in the human fossil record. The question that I addressed in my dissertation is that species definitions tend to take on either ontological characteristics or epistemological ones. Cladistics tends toward ontological definitions while phyletic gradualism tends to gravitate toward epistemological definitions. In my work in the human fossil record, I was tasked with coming up with a definition of modern humans. What I did instead was let them define themselves. I took the modern human data set gathered by W.W. Howells and created a 95% confidence ellipse around that. I then corrected for size and compared a set of fossil humans to the ellipse. In this way I was able to determine whether or not certain fossils that were being called “modern human” by some researchers really were. Many different patterns in the fossil record emerged and the study was quite profitable. The problem, of course, is in extrapolating this definition to the past. Modern humans are at an evolutionary terminus, temporally and so it is easy to define them. Trying to define, say, Neandertals, on the other hand, would be a challenge, despite their characteristic morphology. One thing that was clear was that some some fossils were just outside the range of modern humans because certain traits had not “caught up” with the modern human morphology. Others were way out because too many features were not modern. I could see the mosaic nature of evolution in the human record over the 200 000 years that were represented by the fossils. If ever there was a case for evolution occurring, the human fossil record is it.

The site is undergoing maintenance presently. Commenting has been disabled. Please check back later!