Species and systematics

Human

Good post John. It's a shame to see so many organizations that should know better, as well as news outlets who can be expected to over sell, jumping on "ancestor of all primates" bandwagon. It's not just a case that the framing is wrong or that they are taking the wrong angle on the story, but that the story itself is probably incorrect.

This episode will probably come back to haunt the paleontologists and evolutionary biologists for years to come as creationists use it as an example of "Darwinists" misleading the public.

This is a shame since it is a beautiful fossil, eminently newsworthy in its own right (though perhaps not with so many headlines), and could be a great example for explaining evolution by natural selection to the general public. Instead of this they've gone for a big splash, whuich will no doubt shortly be followed by the story sinking like a stone.

I just hopoe that the documentary discusses the find and the various claims made about it in an more balanced and less excitable way.

This episode will probably come back to haunt the paleontologists and evolutionary biologists for years to come as creationists use it as an example of "Darwinists" misleading the public.

I just hopoe that the documentary discusses the find and the various claims made about it in an more balanced and less excitable way.

All that ancestor-of-humans and missing-link talk is from the media, which misrepresents everything complex. The "reporters" frame everything in the most dramatic light possible. The news practically calls every fossil discovery a "missing link". And don't think the news organizations don't know they're stirring up the creationism debate with their mischaracterizations; they know.

This episode will probably come back to haunt the paleontologists and evolutionary biologists for years to come as creationists use it as an example of "Darwinists" misleading the public.
This was precisely why I thought they made the (sensational) claims they did - this latest find further bolstered (as if it needed it, I know, I know) modern evolutionary theory. The Flat Earthers are always talking about how bananas and peanut butter and what not prove Darwin is a tool of Marxism and Satan, etc; I assumed the over-the-top reporting (IANABiologist, but even I thought the claims a little too pat) was to drive the point home that this find simply reaffirms what we know - evolution happens, happened, will keep happening.
I don't want to give these guys too big a pass, but I think their hearts were in the right place.

Actually, the claim in the published paper is that this
could be the ancestor of all Anthropoids. That is a group
including apes (hominoids), Old World monkeys
(cercopithecoids such as macaque, mandrill) and New World
monkeys (ceboidae). In short of all primates, except the
lemur/loris/galagos and the tarsiers.

This is not a new claim. The fossil is an adapiform, and
whether adapiforms are the ancestors of anthropoids has
been under debate. Experts such as Richard Klein (see
"The Human Career" 3rd edition out just this month) do not
believe, just as you do, the claim can be settled with
fossils. Because shared features might be due to convergent
evolution.

As for the missing link, I think most people consider that
to be the last common ancestor of hominins and the
panini (chimps). From around 7ma - no fossils yet.

So it would be better to say that the ancestor of all primates was probably similar to this and occurring about the same time.

No, if it isn't short, snappy, and definite, a reporter will simplify 'til it is; accuracy comes last.

It is my opinion, and I state as much in my own post on this fossil, that the hype was overdone to the extent that the counter-hype is also overdone. Now, here, I can imagine that a gorilla would take this all personally, and a philosopher could be mainly interested in the hype and framing and stuff, but even on paleo blogs the fossil is getting too little attention.

In other words, we have more blogging about Ida than for the average newly reported cool fossil, by far, but the least said (relatively anyway) about the fossil itself.

Which is why, when I got to writing my version of this, I wrote mainly about the fossil and related issues of primate evolution.

"Ida" may be our greatn parent, but equally it may just be a long lost cousin.

Equally? I would have thought it more likely, and that the specific likelihood would relate to the number of coexisting Adapid species (or perhaps populations).

Actually, the claim in the published paper is that this could be the ancestor of all Anthropoids..

Doesn't the paper claim that the fossil is an Adapid and that, if it is, that is evidence that the ancestor of all Anthropoids was an Adapid - any Adapid, maybe Ida, maybe not.

I think their hearts were in the right place.

Perhaps, but they're paid to have their brains in the right place.

Philosophy and evolution

evolvingthoughts — Tue, 19 May 2009 02:10:28 +0000

Philosophy and evolution

One of the problems that many people have with evolution is not religious, but philosophical. If evolution is true, they think, then we are at sea - nothing is fixed, nothing is determinate, all coherence is gone, as Donne famously lamented of the death of the two-sphere universe and physics. This is, I believe, a valid worry. But it is not new or due to evolution: Heraclitus worried about it, as did Parmenides, and the solutions given by Plato and Aristotle against the atomists were in effect ways to deny that what really counted was changing. They called change "degeneration" or "corruption". The true reality was the forms (εἶδη) that never changed. It was at first not a widely adopted solution, but with the collapse of the Stoic philosophy in the late Roman period, and the rise of Catholic Christianity, it made a comeback and was the "default" view of the next 1200 years.

What in fact does evolution add to the mix of philosophical unease?

Over the past 50 years or so, there have been many attempts to give a general metaphysics of evolution, ranging from axiomatisation (by Mary Williams, at the height of the "theories are axiomatic systems" period*), to "logical necessity" cases (such as Lewontin's three conditions for natural selection), to "units of selection" arguments, most closely associated with George Williams and RIchard Dawkins. In each of these, and other, attempts, there has always been the presumption that there is a fixed hierarchy of ranks and units in biology. These are the "forms" of biology: replicators, interactors, species, genes, cells, and so on.

The odd thing about this is that as people were asserting that essentialism is dead (see the article on species linked above), they were being essentialists about concepts and units and ranks. Ernst Mayr, for example, who asserted that species individually (the species taxon, as he put it) have no essences, nevertheless asserted that the concept of species (the species category) did so. He was an essentialist about the species concept. Likewise, the gene centrism of a Dawkins is essentialist about the replicator concept. And so on.

Now one of the reasons why people adopted the hard and fast categories is that they usually were specialists in groups, such as mammals, birds or insects, where these categories had a real purchase. This is often referred to, mostly by botanists, as the "fur and feathers" or "vertebrate" or just "animal" bias. But another is just that they were seeking what used to be called the Characteristica Universalis, or the most general universal and formal language for the domain in question. It is a general disposition of those in the west to do this (and despite suggestions to the contrary, I cannot see how one might apply the Eastern metaphysics fruitfully in the domain of science). It is a constant temptation to try to ground ideas in unchanging and agential categories. We like species because they do something. We like replicators because they are the ultimate doers. These categories apply in ways that make sense of both the world, and our need for constancy. Coherence is not gone.

Until you stop focussing on the "obvious" cases, and start paying attention to as many as you can find. I have what I call the "esoteric method": look for cases that don't fit the current categories and then go look and see if that is more general than you might think. For example, in his 1942, Ernst Mayr referred to nonsexual organisms as "aberrant" when discussing the adequacy of his "new" "biological" species concept (122, 129). Today we know that not only are most organisms not sexual, which would mean most of them are not arrayed in species, but that the sexuality of species even in the small twig of the phylogenetic tree that is metazoans is not constant: many groups have either got hybridisation, or asexuality, or both. Nor is gene exchange confined to sexual species - between species gene flow is common, and even among asexuals lateral transfer is frequent. In fact the sort of species Mayr expected to exist are rare, except among some groups of vertebrates (oddly, the group Mayr studied, birds, often hybridise).

Over the past 50 years these essentialistic categories have become harder and harder to support empirically, as we have learned of more and more exceptions. Some, such as John DuprÃ©, have argued for a pluralism of conceptions in biology due to the polytypic nature of the instances to which these categories are applied. It's just a brute fact of biology that none of these categories are universal, and so biologists must avail themselves of whatever conception works in a particular case (to make this more concrete: species are sexual isolates when that works, but in, say, bacteria, they are phenetic clusters or something else).

Some years ago, I published an idea that I think might be the resolution to this (2003) in which I argued that species is like any other property of organisms, something that has evolved in its own way. The reason there is no universal notion of species for the same reason there is no universal notion of leg: species, like legs, are the outcome of evolution. In other words, these kinds themselves evolve. This applies also to other apparently universal aspects of biology: genes, or rather replicators, cells, individuals, and so on. It is not the case that, as DuprÃ© thinks, that anything goes, but that there are evolved modalities, as I called them - ways of being whatever it is that we are trying to understand. This applies not only to the organisms and their traits, but to the kinds of organisms, and even to the kinds of kinds. Taxa, units, ranks, entities, systems - all these are evolved, and so to understand what it means to be, say, a bird species or a eukaryote gene, you need to understand the evolutionary relations of that group.

Last year, Peter Godfrey Smith published an interesting book that argues that the sole precondition for a Darwinian perspective on the world is that there are populations. Because we are disposed to see biology in terms of agency, we want agents, but that is, PGS holds, a remnant of the oldthink of teleology that Darwinism replaced. I think he's well on the right track, although he still thinks that this means we cannot have types or classes. I think that classes are merely local and evolved. We are in a reading group covering his book right now, so as we work through it, I'll probably add some more.

One thing I do want to say now, though, is that there is a prior problem knowing what a population is. For instance, to know that an ensemble of individuals form a population, you need, minimally, to show they are of the same species because you don't get a population that spreads across two or more species, unless they are causally connected reproductively (in which case they might be classed as the same species anyway). Moreover, you already need to know the sort of object/organism that counts as an individual for that group in order to identify it as a population. This is not always so easy, in the case of colony organisms. While PGS is rightly arguing that there are no ranks or special units, only populations (which comprise individuals that have heredity and ecological differences, leading to evolution**), it seems to me that he still requires there to be some sort of types or equivalence classes, even if there are no universal kinds of types.

In part, this is something that comes out of the death of the essentialism story: it is often assumed that if one abandons essentialism, one loses access to any kind of equivalence class in biology (i.e., natural kinds; we aren't worried about conventional classes or functionally defined classes), and that is what PGS assumes too. But it is my view that biology always uses types, which are defined or rather ostended by identifying an exemplar and then looking for clusters of properties. This is what PGS says we should be doing, but he does not see these as types. I do. By finding these clusters of properties (and even more the underlying developmental traits and heredity), we are then able to determine what a population is, and what individuals are, by a process of iterative induction (start with a case that is presumably exemplary and then make inductive generalisations from that until they fail).

What bothers people who think in terms, not of binaries as Chris Schoen suggested, but of absolute levels or entities that do not change, is that evolution leaves us gasping and dealing with vague boundaries, shifting kinds and so on. I feel for them, but it is really biology that does this, and always has. What really is novel about evolutionary thinking is that we know not only that the appearances change, but that the forms, and the forms of forms also change. However hard to come to grips with, we must. And the solution to this vagueness is phylogenetic thinking. If you know where a species or an organism is placed on an evolutionary network (allowing for the moment that the tree topology sometimes fails), then you know what sorts of sorts it will fall into, or if you find that it doesn't, that sets up an interesting research project.

More as it occurs to me.

* Williams was a student of the originator of the Axiomatic Method for the sciences, Joseph H. Woodger.

** Evolution includes a lack of change by stabilising selection or developmental entrenchment (which I think may be a subset of the former). We need not presume that selection always causes change (but if there is a lack of change, I think we should presume that is due to selection).

evolvingthoughts Mon, 05/18/2009 - 22:10

Tags

Logic and philosophy

http://www.hedweb.com/bgcharlton/modernization-imperative.html

stasis is dynamic. keep saying that, students of evolution, over and over again.

I Would guess that stabilizing selection is the large majority of selection.

I've worked quite a bit with hybridization in fishes; some thousands of examples in the literature. There are instances where hybrid swarms have been maintained for as long as we have been aware of them. However, I think there are very few instances where hybridization has been important in speciation of biparental species. Also, I think, after examining the evidence, that hybridization between two species usually has little effect on how we view the two species. By this I mean that hybridization has resulted in little or no gene flow between the two species. For some reason, it seems that mitochondrial genes introgress more than nuclear genes.

I don't think there is a useful procrustian universal species concept. Perhaps species is like an electron, sort of a fuzzy sphere of probablity as to position and nature. Said sphere looking different depending on which species is being examined.

Jim, I think you should ask a botanist if hybridisations is rarely the cause of new species in biparental species. Also, you might find that it works differently in different groups - I understand that reptiles have a higher frequency of hybrids than other land verts. Cichlids are also thought by some to be freely hybridising, although from what I have seen that may just mean introgression. Corals certainly. Ferns and fern allies most definitely. Don't know about insects, although I think I saw one on Drosophilids and mosquitoes. The Grants argued that bird speciation by hybridisation is frequent, if not common (and we know ducks massively hybridise). And so on. The apparent lack of it in animals may just be due to the fact that people weren't until recently looking for it.

I think I read that some 25% of higher plant species are of hybrid origin. So obviously a botanist would think differently about species than I do. I have been a semi-serious hobbyist with amaryllis, and various succulents. So I have looked at their taxonomic lterature from my professional perspective. I am clear that botanical taxonomy and fish taxonomy are quite different.

So glad to hear it. But then you know that statements about species in general must be very highly qualified.

I cannot see how one might apply the Eastern metaphysics fruitfully in the domain of science

I'm not inclined to disagree with this with any haste.

But the history of the scientific enterprise is fairly short and recent, and I also wouldn't want to overdetermine what it may and may not encompass down the road.

My main aim in raising the subject is not to try to propagandize for the superiority of eastern over western metaphysics (to the extent these are even valid categories), but to reach for a system of relations with sufficient contrast to our own to throw it into relief, allowing a meaningful evaluation on its own terms. So-called eastern metaphysics is a ready-made world picture, the first that comes to hand.

Lots to click through to here, and lots to chew on.

The odd thing about this is that as people were asserting that essentialism is dead (see the article on species linked above), they were being essentialists about concepts and units and ranks.

Interesting idea about essentialism (or the lack thereof). Perhaps I misunderstand, but I assume it's standard thinking in philosophy that nothing has meaning by itself. No idea, concept, or thought appears to exist ex nihilo alone in a vacuum - the "meaning" of something always stands in relation to other things. An isolated idea is meaningless. The same appears to be true in the physical world (which I suppose would make the entire universe meaningless, if it's truly isolated). A "form" in biology is relative to other forms, in other "species" and forms in different times, as well as forms which exist in a relation of composition (genes, etc). The same is true of physics, at the quantum level. As expressed by Bohr, "Isolated material particles are abstractions, their properties being definable and observable only through their interactions with other systems."

But if you say there are no essential absolutes, that is an absolute in itself, isn't it? Can you really get rid of essentialism?

I think that if Eastern metaphysics is understood in a critical and secular way (which is permissible for eastern metaphysicians) and selectively used when it proves helpful (which is what many of the smartest Chinese and Japanese do, while also appropriating Western approaches as needed), Buddhist and Taoist approaches to anti-essentialism are usable.

One impediment is that all interpreters of the East to the West (regardless of whether they are Western or Eastern in origin) have their axes to grind, and while this is inevitable and not necessarily a bad thing, from the scientist's point of view most of them are grinding the wrong axe. Some of the missionary groups that come over are often the Eastern equivalents of Mormons or Jehovah Witnesses in terms of their take on Eastern philosophy, and Western appropriators can be as bad or worse than that.

Besides anti-essentialism, another thing that evolution brings to philosophy and science is contingency and an open future (expressed vividly in Gould's "A Wonderful Life"). Along with essentialism comes eternalism (e.g. Platonism) -- the idea that everything really real was already there in the beginning, and that new things are just recombinations of old things. One philosopher still thinks that, but he had to conclude that the only really real things are quarks, and that everything else is just a seeming reality.

Some of these themes were developed by Whitehead, whose ideas stand behind Bohm's (mentioned above) and are not widely accepted in professional philosophy.

One of the best attempts to come up with a science-Taoism combination was that of R.G.H Siu in "The Portable Dragon", "The Tao of Science", and "Ch'i: a neo-Taoist approach to life". Siu had a successful scientific career ("MICROBIAL DECOMPOSITION OF CELLULOSE With Special Reference to Cotton Textiles"), mostly at the administrative end, and his development of Taoism is very hard-headed and real-world.

The "Tao of Physics" is probably to be avoided. Likewise the TV show "Kung Fu", which is a primary reference for many.

Probably the best solution to this apparent paradox is Niklas Luhmann's version of systems theory, which focuses on communications instead of structures.

This is very hard to understand (at least, I found it hard to understand, and struggled with it for months)

Peter Andras and I tried to summarize it in the Appendix of our book The Modernization Imperative -

Probably the best solution to this apparent paradox is Niklas Luhmann's version of systems theory, which focuses on communications instead of structures.

This is very hard to understand (at least, I found it hard to understand, and struggled with it for months)

I tried to sumarize it in the Appendix of my online book The Modernization Imperative -

http://www.hedweb.com/bgcharlton/modernization-imperative.html

John E.,

It's been years since I read it, but I think the Tao of Physics gets a bad rap, in part because it is judged based on some of the people who were influenced by it. (As one blogger recently wrote on the same dynamic in reference to another topic [Strunk and White's Elements of Style], this is sort of like blaming the White Album for the Tate-LaBianca murders.) Frijof Capra is a "real" physicist, after all, not a mere mystically inclined populizer, and many of the great names in quantum physics--Heisenberg, Bohr, Pauli--advocated similar metaphysical views, though none of them went on to write systematically about them.

Thanks for the Siu reference; I'll look for him.

Hi John,
I agree with a lot of this. One question, though: where did I say that 'anything goes'? What goes is what shows up in biology. You want to call the clusters of more or less similar entities that evolve within different lineages 'species'. I (and others) point out that these clusters are very diverse, for example with respect to the factors that maintain the similarities to one another of the elements in the clusters and their differences from other entities. Apart from different degrees of comfort with the word 'type' I'm not sure what we need to disagree about.

John

I meant it in a nice way - that scientists can avail themselves of any concept that works for their needs (with which I also agree). You're right - we are not disagreeing. See the disclaimer in the profile...

Punnett on Mendelism and species

evolvingthoughts — Mon, 18 May 2009 20:49:21 +0000

Punnett on Mendelism and species

The wonderful Project Gutenberg has just released a fully HTMLised version of R. C. Punnett's (he of the famous "square") 1911 book Mendelism, which shows how quickly the implications of Mendelian genetics, rediscovered 11 years earlier, were worked through. It's a wonderful read, and anyone with a slight knowledge of biology and the interest to work through the examples can understand it, something one cannot say of texts on science for very much longer after this. I was particularly interested in the following passage, from page 150:

One last question with regard to evolution. How far does Mendelism help us in connection with the problem of the origin of species? Among the plants and animals with which we have dealt we have been able to show that distinct differences, often considerable, in colour, size, and structure, may be interpreted in terms of Mendelian factors. It is not unlikely that most of the various characters which the systematist uses to mark off one species from another, the so-called specific characters, are of this nature. They serve as convenient labels, but are not essential to the conception of species. A systematist who defined the wild sweet pea could hardly fail to include in his definition such characters as the procumbent habit, the tendrils, the form of the pollen, the shape of the flower, and its purple colour. Yet all these and other characters have been proved to depend upon the presence of definite factors which can be removed by appropriate crossing. By this means we can produce a small plant a few inches in height with an erect habit of growth, without tendrils, with round instead of oblong pollen, and with colourless deformed flowers quite different {151} in appearance from those of the wild form. Such a plant would breed perfectly true, and a botanist to whom it was presented, if ignorant of its origin, might easily relegate it to a different genus. Nevertheless, though so widely divergent in structure, such a plant must yet be regarded as belonging to the species Lathyrus odoratus. For it still remains fertile with the many different varieties of sweet pea. It is not visible attributes that constitute the essential difference between one species and another. The essential difference, whatever it may be, is that underlying the phenomenon of sterility. The visible attributes are those made use of by the systematist in cataloguing the different forms of animal and plant life, for he has no other choice. But it must not be forgotten that they are often misleading. [Emphasis added by me]

It's my opinion that the species problem arose around this time when people started to ask the sorts of questions Punnett raises here: what makes the species genetically? It's also worth noting that he distinguishes between the diagnostic genetic factors that are used to identify species, and those that are causally constitutive, as it were. And finally it's worth noting that this is a fully fledged "biological" species concept, 29 years before Mayr published his.

Hattip to Christopher Elliot at Foundations of Science, Sydney

evolvingthoughts Mon, 05/18/2009 - 16:49

Tags

Teeth and a marsupial lion

evolvingthoughts — Sat, 16 May 2009 05:26:07 +0000

Teeth and a marsupial lion

Chris Nedin has another post of great interest (even if it is for a late period, the Pleistocene) which goes into my file of "the older naturalists were great observers", as he shows how modern chemistry supports Richard Owens' diagnosis of Thylacoleo as a carnivore, even though it is in a clade of herbivores.

evolvingthoughts Sat, 05/16/2009 - 01:26

Tags

http://paleocoll.blogspot.com/2009/05/cool.html

'Prerogative of harlots' has a nice additional story:

There is no missing link

evolvingthoughts — Mon, 11 May 2009 07:27:01 +0000

There is no missing link

Again, the press are talking about "the missing link". Let's get one thing clear. There is no missing link. Rather, there are an indefinite number of missing branches. To have a missing link, you need to visualise evolution as a chain. If there's a gap in the chain, then you have a missing link. But evolution, at least at the scale of animals and plants, is mostly a tree. And all we see are individual nodes of the tree, the extant species that form, in Darwin's metaphor, the leaves of the living tree, and the extinct species that form branching points deeper in the tree. But we do not have enough information to know the shape of the tree for all but the smallest twigs and larger branches. There may be, for all we know, millions of missing species. We might have a species that is an ancestor of some other species, and yet not know enough to say that they are indeed the ancestor in question.

This looks to be an exciting find, and possibly it will give us more information about the overall relationships of primates, but it is not the missing link, and it is one of potentially millions of missing nodes of the evolutionary tree.

evolvingthoughts Mon, 05/11/2009 - 03:27

Tags

Biodiversity

darwin

I think Hennig was right in saying that we cannot recognize ancestors; and that branching points in phylogenetic trees are "hypothetical ancestors". You cannot be sure that some fossil was a direct ancestor of any subsiquent species. Therefore, cladists do not understand the concept of "missing link". I do, however, see that geneticists are reconstructing ancestoral genes, which seems anti-Hennigian.

Jim: you assume ancestral states whenever you construct a phylogeny. How is that different from reconstructing ancestors?

Missing link schmissing link, all the same.

That is a good question. I see a difference in saying this is the plesiomorphous state of a character and saying that fossil A is the ancestor of Group A. One has to wonder; however, if we have fossil A which exhibits all of the plesiomorphous character states of Group A, maybe it is the actual ancestor. I think this is one of the problems those of my generation have had in accepting Hennigian assumptions. Cladistics is not a search for ancestors, and denies that they can be recognized as such. This is hard for many to swallow.

Well, yer actual fossil is unlikely to be a direct ancestor, fossils generally being individual organisms that have met an untimely end in some anaerobic and statistically unlikely fashion. I take your point though: there is of course the famous example of the horse family tree to show just how misleading fossil "ancestral forms" can be.

From an analytic point of view, I think if you don't accept some sort of ancestral reconstruction in the nodes of a tree, you can't take the tips seriously.

Of course I agree with your assessment of the "missing link" in scientific usage. However, the term has a more philistine meaning that essentially means a fossil finding that bridges a gap or has explanatory power. This is all personal opinion, but I think when Jane Q. Public is talking about the missing link, this is what they mean.

One point about reconstructing genomes is that there is a fundamental problem of minimum message length reconstructions that is formally analogous to the problem of reconstructing phylogenies - information is lost and can be reconstructed only on the basis of prior likelihoods. In other words, there are numerous ways that the present sequences could have been evolved, just as there are numerous ways the present taxonomy could have been evolved. We have to just live with the fact that the past is another country.

I fail to see how what we do not know about paleontology affects what we do know about neontology, Chris.

John: er, smaller words please? Five years ago I cudn't evun spell bilologist and now I are one, etc.

Ok, suppose you have two gene sequences from related species and you are trying to reconstruct the ancestral sequence. For each change, one or the other might be the changed one, or they might both be changed. Even if they are the same, they might have paralleled each other, and neither be the ancestral sequence. And that is not taking into account inversions, pseudogenes, and laterally transferred sequences. So the number of ways that a sequence alignment may have arrived at that point are manifold, indeed astronomical. Repeat and rinse for every gene in the species. The likelihood that the reconstruction is correct is vanishingly small.

To pare down that space of possible histories, just for two species, requires major assumptions and theory, and none of that can be independently supported except by analogy with other cases, and so the optimism Jim shows is, I think, unfounded.

Were them words easy to follow?

Were them words easy to follow?

Perfect squire, even I could follow them and I aint a bilologit.

When idiots start talking about the "missing link", I deliberately misunderstand and tell them about the telomere block "link" in the middle of human chromosome 2, corresponding to the fusion site from primate chromosomes 2p and 2q. "See? The link has been found, so it's not missing."

This usually results in further incoherence, but at least the idiots learn one more little something.

Much more gooder, thanks John.

I'm a bit cynical about the approach that some molecular people have to evolution, so I guess I was thinking more of complex ancestral traits than gene sequences. Reconstructing ancestral character states (in the "organ that does X" sense) is something I've recently become interested in for the purposes of understanding how said traits arise.

I have coconspired with two different sets of DNA workers to generate phylogenetic hypotheses. In each case, I was sat down and bored to tears with an hour-long monolog about the problems and mistakes one faces in doing DNA. The lecturers were biologists first and DNA workers secondly, which may not be universally true. These experiences make me suspect that people trying to reconstruct ancient genes are well aware of the difficulties involved. I also suspect the problems John mentions are a small part of the total. Anyway, it is not something a good Hennigian would consider attempting.

See, now there I disagree with you. It's worth attempting. It's just not absolute truth (because information is lost over time). Phylogenetics is a preliminary step to reconstruction of the past, not the attainment of it, and all such reconstructions are tentative in direct proportion to the evidence available (phylogenies can rule out some histories) and the assumptions used in the models on which the reconstructions depend for their likelihood assignments.

Forgive me if i am incorrect for any of my comments because i am only fourteen years old and lack any experience in this field of knowledge, but i would like to say that the theory of a tree is quite accurate but could include more detail because it doesn't cover the branches of sub-species and the then the extinction of some sub-species and the seperation of a species and a sub species as that sub species becomes an entirely different species all together.

If people really just have to have a missing link, Australopithecus afarensis is probably about as close to one as we're ever going to get.

I guess the idea is that the chain leading to humans
has nodes where other species branched off. The latest,
Neanderthals, branched off at H.Heidelbergensis.
In that sense, there is a missing link, in the sense of
no fossils, at the node where the Panini (chimps) branched
from the Hominini (humanoids), around 7ma. Not a big deal,
but finding such a fossil would help us understand the
beginnings of the hominins better.

Ida seems to be hyped way beyond credibility. The claim
in the popular press is that it represents a missing link
(a node where primates branched off). The claim in the
published paper is far weaker. The fossil in an
adapiform, which may or may not be the ancestors of the
Anthropoids (apes, Old World Monkeys and New World
monkeys).

Got a question here all,

It would seem that as large as the "Chain" of Human evolution would be it would be near impossible to find a "missing link". I understand the desire to study and search for our origins but would it not be better to study and put our efforts into learning how we are currently developing?

To be honest I am a "creationist" but I think there is no harm in having an open discussion, I have no desire to "debate" my own beleifs, being that they are based on pure faith something I find difficult to debate any way. I have always felt it important to get a clear picture of what the "other side" understands.

I also find it hard to doubt the fossil record, I can totally except that Homo Sapiens have "cousins" it has at times caused difficultlys with other "Creationist".

Any ways any response would be welcomed!

Thanks
Eric

To pare down that space of possible histories, just for two species, requires major assumptions and theory, and none of that can be independently supported except by analogy with other cases, and so the optimism Jim shows is, I think, unfounded.

The first biological species concept

evolvingthoughts — Sun, 10 May 2009 20:53:35 +0000

The first biological species concept

Before this text in 1686, the term species just meant some sort or kind of organism. It was a Latin word in ordinary use without much meaning in natural history, but then arguments began whether or not there were one or more species for this or that group, and so it became important to know what was meant by the term in natural history. That is, a distinctly biological concept of species was needed, and John Ray gave it here:

The translation is this:

In order that an inventory of plants may be begun and a classification (divisio) of them correctly established, we must try to discover criteria of some sort for distinguishing what are called “species”. After long and considerable investigation, no surer criterion for determining species has occurred to me than the distinguishing features that perpetuate themselves in propagation from seed. Thus, no matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as to distinguish a species … Animals likewise that differ specifically preserve their distinct species permanently; one species never springs from the seed of another nor vice versa. [Historia plantarum generalis, in the volume published in 1686, Tome I, Libr. I, Chap. XX, page 40 (Quoted in Mayr 1982: 256)]

So now you know what was said and where. Note that this is not a "biological" species concept - there is nothing here about interfertility; it is a generative conception of species - things are one species if they generate the same forms reliably.

evolvingthoughts Sun, 05/10/2009 - 16:53

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http://penelope.uchicago.edu/ross/ross221.html

He is clearly not giving spontaneous generation the time of day. I think his definition is biological, as opposed to mystical, in that it treats the biology of the organism as definitive. Is this definition not subsumed, or assumed, in the present day Biological Species concept? We all expect interbreeding within a species to produce more of the same, and thus see no reason to carry on about it?

As a side issue one of the things I most admire about some of the thinkers of this period is the way in which their research led them to reject certain claims which had reinforced religious belief. Spontaneous reproduction was one such claim.

Dr. Tancred Robinson (a close friend of Rays) really put the myth of spontaneous reproduction to bed despite the fact that one other very close associate of both Ray and Robinson, Edward Llwydd used the myth to place fossils in a firm biblical framework.

Sir Robert Moray had already reported the existence to the Royal Society of spontaneous reproduction at work in the Western Isles of Scotland. He had gazed through a convex glass at tiny Barnacle goose embryos in their shells plucked from a rotting log drifting on the North Atlantic. Robert Moray may have used scientific instruments to see more clearly and legitimise his beliefs in a supernatural realm but his eyes were blinded by faith.

The Goose barnacle claim goes back to the mid-12th century at the latest. I have written on it before here and as you know, here. But it is not at all clear to me that this is due to religious belief. Spontaneous generation was a widely held belief dating from Aristotle. I think it likely that people saw what theory demanded they should see (which makes Robinson and others like Redi even more admirable); and that religion then used these ideas for its own purposes (like allowing the bishop to eat the Barnacle Goose on Friday, because it was not meat but fish).

I may be wrong John, research is not finished but with any sort of belief like this they are generally subject to change so it's meaning in the 12th cen is not necessarily going to be the same as the late 17th cen.

I concentrate particularly on belief at this time in Scotland.

One example would be Alexander Ross ( Scots minister) and his discussion of the Phoenix in Arcana Microcosmi, in which you see many of the usual subjects all grouped together to reinforce the belief, the phoenix, the silk worm, and the barnacle goose. Their was certainly an effort to make the Phoenix appear more barnacle goose like from the 16th century by emphasising it's relationship with the palm tree.

Close to the end of his discussion Ross "The like I may of the Phoenix, which is a miracle in nature, both in his longevity, numerical unity, and way of generation. And in this wonderful variety the Creator manifests his wisdom, power and glory."

He even uses alleged comparative anatomy at one point to prove the case. Ross is the kind of guy Tancred or Ray have to contend with. His use of the subject seems pretty clear.
The words wonder, wonderfull and god do tend to pop up in Scottish texts at least in relation to the barnacle goose more than once in this period.

If you look at Robert Boyles little experiment in Scotland to prove the existence of a supernatural realm by empirical methods you find in related correspondence by the like of Samuel Pepys and others a particular interest in what he terms the clay goose (from the Scots Clakis goose or Barnacle goose)

Martin Martin who wrote one of the earliest ethnological works in Scotland on the western isles taking a particular intrest in local belief is completely silent on the barnacle goose despite the fact it was at the time one of the most famous aspects of belief from this area and remained so for a considerable period (The barnacle goose forms an important part of the introduction to J.F Campbellâs collection of folktales of the western isles as Robert Murray had recorded the belief before)

Martin Martin is out to demonstrate the existence of a supernatural realm but he uses prophecy instead. His only comments on Sir Robert Murrays trip was to deny he had visited. Martin's views came under considerable attack in London from thinkers not particularly drawn to religion. His unusual silence on the barnacle goose suggests it had lost all credibility as a supernatural phenomenon by this time in London and he was trying to watch his back.

But I have some work ahead to finish things so my view may change but looks resonable for Scotland at least at the moment.

p.s Ross's text on the Phoenix and barnacle goose

p.p.s Sir Thomas Browne's remarks on the Phoenix (It's what Ross was responding to.

http://penelope.uchicago.edu/pseudodoxia/pseudo312.html

Browne and Ross do seem to go on about copulation and species a lot; Browne certainly does seem to do a fair amount of head scratching on the subject in his works. But thats not my area of knowledge.

"PhÅnix hath no distinction of Sex, and therefore continueth not his species by copulation, as other creatures do."

One of the joys of regularly visiting Johnâs blog is that one comes across many well informed and intelligent people; I strongly suspect that this is the only place in the inter-tubes where one could meet somebody holding forth informatively about Alexander Ross. However I would be very careful about attributing religious motives to Rossâ utterances.

Ross was an ultra-radical conservative and was against anything and everything that was either new or foreign or even worse both. My favourite piece of Ross is a passage in one of his writings where he complains vehemently about the introduction of new fangled French sauces into the English cuisine. Iâm not sure what enrages him more the fact that the sauces are new or that they are French! He is of course referring to the French roux sauces which were introduced into England in the early part of the 17th century. (Please donât ask me for a source for this, as Iâm not sure if I could find it in a hurry and I donât have time at the moment to look for it)

Rossâ motives are those of a reactionary and as such not necessarily religious, which is not to say that you may not be right in this case but I would be very careful before committing myself if I were you.

The science of systematics

evolvingthoughts — Fri, 08 May 2009 22:34:57 +0000

The science of systematics

As the science of order ("taxonomy"), Systematics is a pure science of relations, unconcerned with time, space, or cause. Unconcerned with time: systematics is non-historic and essentially static; it knows only a simple juxtaposition of different conditions of form. Unconcerned with space: geographical factors are not primary criteria in the definition of taxonomic units. Unconcerned with cause: systematics has no explanatory function as far as the origin of the system is concerned; it is merely comparing, determining, and classifying.

Borgmeier, Thomas. 1957. Basic Questions of Systematics. Systematic Zoology 6 (2):53-69.

evolvingthoughts Fri, 05/08/2009 - 18:34

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Amen. Ah, the great Father Thomas Borgmeier (1892-1975).

Wow, you are really into ancient history! That was published nine years before I joined the Society.

I have just written a response to your post on Borgmeier (1957) here.

A new online philosophy of biology journal

evolvingthoughts — Fri, 08 May 2009 19:01:34 +0000

A new online philosophy of biology journal

It's called Philosophy and Theory in Biology. This is based on some heavy hitters: Massimo Pigliucci, Jon Kaplan, Alan Love and Joan Roughgarden are the editors, and the editorial board looks like a Who's Who of philosophy of biology. No apparent page charges, and it's online only (I hope they take care of the enduring archiving), but it looks interesting. How it differs, apart from being virtualised, from Biology and Philosophy, Biological Theory and the several other more specialised journals I can't yet say.

evolvingthoughts Fri, 05/08/2009 - 15:01

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Biodiversity

Logic and philosophy

Various divers thingies

evolvingthoughts — Wed, 06 May 2009 16:45:53 +0000

Various divers thingies

My union is calling a strike next Tuesday. I'm not sure what to do. I don't teach, and have no administrative duties, so should I stop thinking ~~from~~ for 8 hours? I'm not sure the administration would notice...

Rob Skipper at hpb etc. has a series of podcasts from the series of lectures on Darwiniana that were held there recently. They include John Beatty, Roberta Millstein and Ken Waters, all serious folk in philosophy of biology (although Roberta, at least, is not serious all the time). From the sublime to the faintly absurd, you can also see my talk in Lisbon, one of them, anyway, at Ciencîas Viva, here. I always say I am smarter in print than in person, and here you will find out why. Some technical difficulties messed up the first few minutes.

Etherwave has a nice post on the setting up of the Cambridge Scientific Instrument Company by none other than Charles Darwin's son, Horace.

Quentin Wheeler is touting for publicity by naming a beetle after Stephen Colbert. Just because the arachnologists managed to get airtime that way, Quentin...

Ireland is reviving blasphemy laws. Sensible people disagree. I might have to desecrate a cracker in Dublin...

Now that NASA head Mike Griffin is gone, people are finally able to review the absurdities of the Ares I launcher. I think that the existing heavy launchers will do fine, and that they should develop a very heavy launcher like this.

evolvingthoughts Wed, 05/06/2009 - 12:45

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Politics

religion

Technology

trashcan categorial

Your strike responsibility can be to feel self righteous: if you could be striking, you would be. If there is a picket line, you can carry a sign and shout slogans. Or sing The Internationale.

If you desecrate a cracker, someone will surely start that Wiki page for you. It could be me, but then I'd have to learn how to do footnotes.

My singing could set back academic rights a whole century.

I never figured out Wikipedia's footnotes either.

Your talk gets off to a promising start, but for technical reasons I'm struggling to listen to it. I only get audio, no video, and also not appearing is any sort of pause button that I could use to let the buffering get ahead a bit.

I could download the whole thing, but that is one enormous file.

Was that a stunt double or do you write much older than you appear in person (on video)?

Oh, you can stay...

Three cheers for the Irish Times! (They for many years carried Brian O'Nolan/Flann O'Brien/Myles na gCopaleen's column "Cruiskin Lawn," judged by James Thurber "the funniest newspaper humor column in the world": O'Nolan tried to emulate Shaw by writing his novel "The Hard Life" in such a way as to tempt the authorities to seize it under the Irish censorship laws of the time, but someone tipped the police off and they let it go.

Blasphemy laws are a [redacted] idea!

---

As for the strike... whenever the local at the University of Melbourne calls a strike, the admin sends around an e-mail asking those academic staff who are going to go on strike to please inform them, so they know whose pay to dock.

I thought the strike was Tuesday past? And it Didnt happen.. Come to manning, have a few beers and let people pick your brain

I would like to say something clever and original but as usual Douglas Adams got there first:

[...]

Majikthise: "We, are Philosophers."

Vroomfondel : "Though we may not be."

Majikthise: "Yes we are."

Vroomfondel: "We are quite definitely here as representatives of the Amalgamated Union of Philosophers, Sages, Luminaries and Other Thinking Persons, and we want this machine off, and we want it off now!"

[...]

Vroomfondel: "We'll go on strike!"

Majikthise: "That's right! You'll have a national Philosopher's strike on your hands!"

Deep Thought: "Who will that inconvenience?"

You should engage in anti-thinking, not non-thinking. For eight hours you should peddle creationist clap trap, such as that found at Answers in Genesis or Ray Comfort's Blog. You should also periodically yell "Banana" or "Intelligent Design is science" at the top of your lungs.

My brain wouldn't recover from that. Maybe when I was in my twenties, but that would be the death of whatever rational thinking I still have. Instead I'll think about things I'm not paid to think about, like international politics or art.

Two observations about Ireland's reviving their blasphemy laws. First, don't they know that blasphemy is a victimless crime? And second, from reading your story, I learned the Irish word for "idiot",which certainly applies to the politicians who are reviving said blasphemy laws!

Linnaeus on evolution by hybridism

evolvingthoughts — Fri, 01 May 2009 23:54:18 +0000

Linnaeus on evolution by hybridism

It is often stated in the literature that Linnaeus late in life turned to an evolutionary view based on hybridisation (e.g., Clausen, Keck and Hiesey 1939). I myself have repeated this, but as always it's worth looking at the actual text. Unfortunately I have so little Latin that I can't even use pig Latin, so it is great to find, yet again, that archive.org has it in an English edition published in 1783. I love archive.org. Deeply.

It's in the context of what he bases his system on, the "fructification" of the plants; i.e., the reproductive organs:

26. The PRINCIPLE of Fructification, the Foundation of Botany, should be traced higher.

Problem: we may suppose God at the beginning to have preceded from simple to compound, from few to many! and therefore at the beginning of Vegetation to have created just so many different plants, as there are Natural Orders. That He then so intermixed the plants of these orders by their marriages with each other; that as many plants were produced as there are now distinct Genera. That Nature then intermixed these Generic plants, by reciprocal marriages, (which did not change the structure of the flower) and multiplied them into all possible existing Species; excluding however from the number of Species, the Mule-plants produced from these marriages, as being barren.

Each Genus therefore is natural, Nature assenting to it, if not making it.

The Character therefore never constitutes the genus, but is itself diligently to be constructed according to the Genus of Nature.

Kindred Plants of the same mother, are to be known in respect to the Genus by the flower, or displayed plant, when the reciprocal undulterated marriage leaves the Fructification entire; but in the species are to be diftinguished from their sister-companions, produced by a different father, according to the Herb.

Thus the Diagnosis of a plant consists in the affinity of the Genus, and in the difference of the Species.

The Name of a plant therefore, that it may refer to each diagnosis, is double:

the Generic Family Name,

And the Specific trivial Name,

under which latter are the vague Synonymies of authors.

The Botanist, in following the Classifications, is lead to the named Genus by the Characters of the displayed plant or flower; to the appellation of the Species by the Differences of the Larva or herb; and thence to its Synonymies; from these to Authors, and thence to every thing, which has come to us from our ancestors on the subject. Thus the plant itself tells its Name, and its History amid such a multitude of species, and of individuals; this is the great purpose of Botany, the invention of the present age, to the completion of which all true Botanists will contribute their labour.

In other words, Linnaeus makes the following claims:

1. All propensities were created once, as the "Natural Orders", and recombination of these generates genera (which are in his eyes natural, unlike modern views of taxonomic ranks above the species level), and again into species.

2. To be an infertile species, a "mule", is not to be a species at all. This means that for Linnaeus, a species is a reproductive group. I therefore must take back what I have elsewhere said about Staffan Müller-Wille's (2007) claim that Linnaeus had a "biological" species concept; indeed he can be interpreted that way. Too late for the book, alas...

3. Diagnosis relies upon "affinity", and not a single Character, at least in a natural system. I am coming to the conclusion that "affinity" is a kind of vaguely expressed notion of the sum of homologies between taxa, and it become extremely important in the later writings of taxonomists, especially in French and English taxonomy, as botanists attempted to create a "natural system" along the lines of Jussieu. That Linnaeus mentions it here is of great interest to me.

4. Note that Characters are not the essence of the Genus or Species, but "lead the botanist to the Genus". They are diagnostic rather than constitutive. The famous botanist John Lindley also makes this distinction explicit in his Introduction to the Natural System in 1831, so the term's life exceeds just the Linnaean scheme. I believe this was greatly influential on Darwin's ideas, as Polly Winsor also does in general terms (2009), as I have discussed previously.

This is a later view of Linnaeus', not his views that made his career. It became interesting after Darwin made transmutationism respectable, and people went looking for precursor views. He is not, however, in any real sense an evolutionist - the new species arise as the recombination of prior characters and mechanisms that already existed. There's no novelty.

References

Clausen, Jens, David D. Keck, and William M. Hiesey. 1939. The concept of species based on experiment. American Journal of Botany 26 (2):103-106.

Linnaeus, Carl. 1783. A system of vegetables, according to their classes orders genera species with their characters and differences. 2 vols. Vol. 1. London: Botanical Society, at Lichfield. Printed by John Jackson, for Leigh and Sotheey. Original edition, Translated from the [1774] thirteenth edition (as published by Dr. Murray) of the Systema Vegetabilium of the late Professor Linneus; And from the Supplementum Plantarum of the present Professor Linneus.

Müller-Wille, Staffan, and Vitezslav Orel. 2007. From Linnaean Species to Mendelian Factors: Elements of Hybridism, 1751-1870. Annals of Science 64 (2):171-215.

Mary P. Winsor (2009). Taxonomy was the foundation of Darwin’s evolution. Taxon, 58 (1), 1-7

evolvingthoughts Fri, 05/01/2009 - 19:54

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