Saturday 7 February 2009

Clade and Grade- Part One: Re-interpreting Life

I thought I'd take advantage of this period of being gagged but not bound to write about our current system of looking at life and some of the errors it leads is into thinking.

There are two ways of viewing the so-called family tree of life. The older form, popularised by Ray Lankester, emphasised 'Grades'.

For example, we talk of mammals having evolved 'from reptiles'. In other words, our ancestors passed through a reptile stage. Some stayed put, and some moved up a grade. We then talk of man having evolved 'from apes'. Again, it implies that our ancestors moved on from being apes, while other apes stayed put.

It is, of course, misleading. Because when we then say 'reptiles appeared in the late carboniferous', we tend to look at existing 'reptiles' and see them as having been there, when we were not. We look at a Chimpanzee and think of him as having been around millions of years before we were.

So the grade approach can mislead. Besides, it focusses so often on arbitrary external features. After all, the only way to distinguish a mammal from a reptile is that a mammal is a warm blooded amniote with fur, the reptile is a cold blooded amniote without fur.
Classification of the amniotes is flawed in this regard. Mammals and birds are amniotes with certain features, all those without 'stay' at the reptile grade. It is a bit like Baldrick's famous dictionary definition of a dog as 'not a cat'.

Recently classificaation has moved to cladistic definitions, sorting animals into groups based on evolutionary relationship. In many ways, it has failed to reach popular conception yet, certainly at the end of the tree where it is most pertinent. Because we have historically looked at the tree and graded it 'like us' 'less like us' 'not like us at all'.

But oddly, there does come a point when perhaps the grade approach is the correct one. When we can actually say 'the descendants of this organism that did this are QUALITITIVELY different from it's ancestors and those of it's descendants that didn't. In other words, it is a new form and we are right at this point to say that this particular organism around today WAS around when we weren't.

But we need to get to grips first with what we mean by life.

To begin with, there was no mystery to that- it was just what caused it. Living things were things that seemingly did things; grew, reproduced, died- without a motor apparently driving them. There seemed to be a ghost in the machine somewhere, because the driving motor wasn't identifiable.

So plants and animals were alive. They were DOING things, but how they did them, was a mystery. The force was unseen.

Now, of course, we know the answer. Metabolism. The curious trick whereby life manages to create chemical reactions without combustion. It's a clever chemical reaction. It is exactly the same as all change, all movement anywhere. It is an electromagnetic reaction like fire, but without the flames.

But- here comes the wierd thing- now we know that, we have a problem. Is our definition of life then, anything that is driven by a metabolism?
No. Now we no longer know how to define it. Because we accept that this process must have started BEFORE metabolisms. A metabolism that didn't replicate, will have died. So the start, was the replicator. Metabolism came later.

And where do we classify viruses? Right now, we classify them outside life. We debate whether to expand the definition of life to include them. Mainly because they are no cellular forms. Just free standing proteins, if you like. But they replicate. The thing is- you can create a new virus in a lab. So if we include viruses as life, we then find that the statement that man can create life becomes true. Only- it isn't, in the sense we can't actually replicate the process that resulted in US being here.

In fact, including viruses as life only emphasises the qualititive differences between us and the virus.
But the real point is, we have long since gone past the point where the tree of life is tenable. Bacteria are not in fact our long distant cousins. Components of our cells are. That's the point. Multicellular life is not related to unicellular life, the cells of multicellular beings are.

I would say, let's start at the begining, but in subjects such as this, that's not always helpful. So let's in fact start at the end. Us.

We are the species Sapiens of the Genus Homo of the family Hominidae of the order PRimate of the class Mammalia of the phylum Choradata of the kingdom Animalia of the Empire Eukarya.

Let us start with our species.

We are the only species in the genus, so we don't spend too much time thinking abput the relevance of species.
Generally, lifeforms are described as being members of the same species if they breed true in natural conditions.
The point is, usually members of the same genus but different species CAN breed, though not always create stable hybrids. Lions and Tigers CAN breed and have been bred in captivity.
Indeed, very often the only thing that marke off a separate species is they don't choose to breed and will never do so naturally. But biologically they usually can.
By which I mean, we probably wouldn't be sexually attracted to Homo Erectus women if they still lived and therefore wouldn't as a whole choose to have sex with them. But we probably COULD have done and such unions WOULD have produced children.

Species in the same genus are usually far enough away to not be sexually attracted to eachother, but sex between them is biologicaly feasible.
So species, really, has significance only for studying cultural populations. It isn't the true biological boundary between lifeforms.

The genus is the most useful identifier of a distinct lifeform. But in fact, family is useful too. The animals in the Felid family are all basically cats. The animals in the canid family are all basically dogs. And the animals in the Hominid family are all basically apes.

One is tempted to reccommend scrapping the latin specfic for the common descrption of a lifeform and restricting it's usage merely to zoologists, breeding experts, etc. And adding the colloquial English form of the family in front of the genus as the common identifier of the group.

Thus both dog and wolf would become Dog Canis, while the fox would become Dog Vulpes. The common cat would become Cat Felis, whilst the lion and the tiger would become Cat Panthera.

And what would it mean for primates? Well, the Hominid family contains us, the Chimps, the Gorillas and the Orangs. Gibbons form the family Hylobatidae, which now has more than one genera.
What would we call these?
Well, there is only a problem if you want to continue denying the obvious. I would say the answer is, stop calling the Gibbon an ape. Then the common Gibbon can be Gibbon Hylobates.
And then the Hominid family become...

Ape Pongo (The Orang Utan), Ape Gorilla (The Gorilla), Ape Pan (The Chimpanzee) and Ape Homo (Man).

Personally, I find this categorisation much more helpful. And honest, in that it puts Homo firmly amongst the apes- not descended from apes, but one of them. Which is what Homo is, a genus of ape.

Moving to having Family and Genus as the key identifiers, rather than Genus and Species is far more helpful, I feel.

Now we come to Orders. To be honest, the Orders are in total disarray at present. Modern research has shown that many orders, especially in the mammalian class, were not actually composed of related creatures- or that they were more closely related to creatures in other orders than ones in their own order. The Order Insectivora is no longer recognised, for example. We now have a plethora of mammalian orders, seemingly because we designate every order as consisting of mammals that have formed seapate lineages from the start of the Paleocene. In no other class do we plump for so recent a divide.

So I would argur for re-merging of mammalian order to form a smaller number of larger orders, based on true genetic relationships.
Of course, some of those new orders would surprise many not familiar with recent advances in genetic knowledge.

The basic division of the Mammals in Montremata, Marsupiala, and Placentalia would seem to be sound. However, I would agree with those who suggest that the Xenarthra (Sloths and armadillos basically) are so distantly related to the rest of the Placentalia, that they should form their own division, consisting of two orders, whilst the rest of the Placentalia, the Epitheria, form another division with extant orders as follows;

Archonts- Includes us. The whole of the current order Primate, plus the Tupiaidae (tree shrews) and the Colugos, or flying lemurs.

Glires- The old order Rodentia, basically. Lagomorohs were sparated in the last fifty years, Glires simply recreates that.

Cetartiodactyla- Already treated as one order. The even toed ungulates (ruminants, pigs and hippos) plus the whales, basically)

Chiroptera- Bats.

Zoomata- Quite an unusual order, since it contains animals that don't appear related, but in fact are. It is a merger between the Carnivora (dogs, cars, bears, seals, walruses, weazels, pandas, racoons) the Pholidota (spiny anteaters) and the Perrisodactyla (horses, tapirs and rhinos).

Erinaceomorpha- Hedgehogs.

Sorincomopha- Common shrews, moles, solenedons, etc.

Afrosoricidae- Golden moles and otter shrews

Macroscelidae- Elephent shrews.

Tubelidentata- Aardvarks.

Paenungulata- Elephants, dugongs, hyraxes.

It will be noted from this system, that several orders consist entirely of creaures that are a bit shrew like. Naturally. The basic ancestor of all these orders was a bit shrew like. So we should expect that. When we look at a shrew, we are looking at what the early mammals looked like. So looking like a shrew doesn't really say what other mammals a shrewlike thing is related to.

But a tree shrew is OUR type of mammal, and an Elephant shrew isn't. In this classification, the general term shrew now acquires a different meaning. It means 'basic mammal who most closely ressembles the common ancestral mammalian form'.

As to where we put the extinct order of mammals? Well, the Creodonts and the Cimolesta clearly belong to the Zoomata. The Toxodontia and the Litopterna are the only ones now seemingly without a place. My guess is that the term Notoungulata used to group them together is still valid in this scheme, they would appear to have been divergent fot at least as long as the Archonts and the Glires. As to the Condylarthra, I don't know. But at some point surely, that mystery will be solved.

Now we move to the next level, the problem of Class. Here I have to agree with the Cladists, the classification of the chordates suffers a major problem. Though only one. Fish are no longer treated as one class, because it isn't contentious splitting them up into classes which reflect their evolutionary relationships.

And modern Amphibians clearly ARE closer related to eachother than they are the three classes grouped together as Amniotes. It is the classification of the amniotes that is woefully misleading.

Because the common ancestor of the mammals and the 'reptiles', we call a reptile, but all it's descendants have changed, it's just in different directions. To classify these descendants correctly, we actually have to look at different distinctions than we are prone to do.

The problem starts with our ancestors, creatures we call 'mammal like reptiles'. This is misleading. They weren't mammal like, because they had no fur and laid eggs. Nor were they ancestors of reptiles, all their living descendants are mammals. In fact, reptile like mammal would be more truthful. They looked like what we call a reptile, but actually they were on the branch of the tree that led to us.

So where do we put their fossils? Mammals or Reptiles?

In fact, there is a clear way we can distinguish between all amniotes, a basal distinction that separates them right the way back in the Permian.

Skull structure. Mammals have synapses, the rest don't, the rest have variations. And the Testudines, or tortoises, turtles and their kin are different again.

So we can fairly classify the amniotes into three groups. One of those groups contains all mammals and no other living creature that isn't a mammal. So in a sense we could keep calling that class Mammalia. Except it leaves those curious acestors that we call mammal like reptiles when in fact they are reptile like mammals in a strange place.

Cladists group mammals and mammal like reptiles together as Synapsids and I don't think it would be wrong to call the class containg them Synapsids and dispense with the term Mammalia. There are viviparous creatures other than mammals for a start and for another, being viviparous is not even a distinguishing feature of existing mammals. Fur is. But perhaps it would be more appropriate to describe the Class Synapasidae as 'Amniotes possessing synapses, the extant members of which class all possess body fur'.

If one then elevates the Testudines to a class in their own right, we are now left with the Sauropsidae, the remaining reptiles and birds.

What a curious mismatch. Or is it?

Not, perhaps, as much as first appears. There are still two basic divisions here, though I think it is hard to justify birds as a class in their own right. Birds are the sole survivors of the Saurischian dinosaurs and we are actually seeing now that many members of that order possessed feathers, though they couldn't fly. It seems that feathers were originally evolved for other purposes, perhaps for warmth and for mating purposes. Birds are in fact related to Crocodiles and one can see the ressemblance if one looks.

One is tempted to create two classes out of the Sauropsidae;

Archosaurs- Including all birds, crocodilia and the extinct orders of dinosaurs.

Lepidosaurs- All remaining reptiles, including Ichythosaurs and Pterosaurs.

Of course, one could go through the whole so called tree of life doing such alterations. And yes, I guess that's where biological classification is going.
But do we need to look at more serious revisions?

Do we need to look at serious clarification of what we mean by life and perhaps remove that term from out thinking altogether?

Put simply, is relating man to bacteria like trying to put quarks in the periodic table?

That is what the next post will look at.


Anonymous said...

Taxonomy is a very complicated endeavor, and I'm not one really to judge how others have grouped things in the past, more or less. I would say, however, that these sorts of connections are human centered, i.e., based on our understanding of how things work, not how they actually work, or relate to one another.

I'm also unclear as to why you think there is no kinship between one-celled and multi-celled organisms. Can you cite a source for this? Because frankly, I've always heard the opposite touted as probable.

Anonymous said...

Not quite what I'm saying. What I'm saying is, that multi-celled life is something new.

It's a bit like atoms and quarks. The elements are a scale upwards from sub-atomic particles.

What I'm arguing is that our type of live starts with multicellular life. From then on, you have TWO types of relationships; the relationships between the multiceullar forms, and the relationships between their individual cellular components.

It is not US that is related to the foraminifer; it's our cells that our. We're just colonies of distant relatives of the foraminifer.
That's my point. What I'm saying is that we should classify the cells of multicellular beings as being the actual relatives of unicellular lifeforms. And the human body contains 140 differnt types of cell. So that's actually 140 symbiotic types of unicellular lifeforms living together in a vast colony.