Happy Halloween!

Primates and Such

My next post on ID and Human Origins won’t be till Monday. In the meantime I thought I would do a post on some background information on primate evolution. Just for fun, I will do this in the form of a question and answer session.

What is a primate?
That is actually a good question and the answer is quite complicated.

What do you mean? Aren’t monkies monkies?
Well yes, but it’s more complicated than that. It is easier to define modern living primates. Primates as a group do share some unique, universal (among primates) features not shared by other mammals. Unfortunately, the also share features in common with other mammals.

Could you give an example of a unique (or diagnostic) feature that separates one mammal group from another?
Sure! The double pulley configuration of the astralgus (a bone in the hind limb)is diagnostic of artiodactyls.

But, what about primates?
That is a good question. Mivart first defined the order primates. His defination was:

Unguiculate, claviculate placental mammals, with orbits encircled by bone, three kinds of teeth, at least at one time of life; brain always with a posterior lobe and calcerine fissure; the innermost digit of at least one pair of extremities opposable; hallux with a flat nail or none; a well developed caecum; penis pendulous; testes scrotal; always two pectoral mammae.

Wow, that’s a lot!
Actually there is more. Mivart gave his definition in 1873. In 1959 Le Gros Clark added to it:

Preservation of generalised limb structure with primitive pentadactyly (five fingers). Enhancement of free mobility of the digits, especially of the pollex and hallux (both used for grasping). Replacement of sharp, compressed claws by flat nails; development of verysensitive tactile pads on the digits. Progressive shortening of the snout. Elaboration of the visual apparatus, with development of varying degrees of binocular vision. Reduction of the olfactory apparatus. Loss of certain elements of the primitive mammalian dentition. Preservation of a simple molar cusp pattern. Progressive expansion and elaboration of the brain especially of the cerebral cortex. Progressive and increasingly efficient development of gestational processes.

That seems pretty thorough. Is there more?
Yes, there is.

I was afraid of that.
Please don’t interupt. In 1967 Napier added two more:

Prolongation of postnatal life periods. Progressive development of truncal uprightness leading to a facultative bipedalism.

That’s a lot of information, where did you get it?
Mainly from R. D. Martin’s paper “Primates: A Definition”

Doesn’t Luskin cite some paper’s by Martin?
Yes, he does. I will talk about that Monday.

So what’s the problem with the above definition of primates?
There are two problems. First, some of the above are actually trends, some of which are not not features. Instead they refer to developments found only in some members of the group (remember, we are not trying to trace ancestor-descendent relationships at this point. We are trying to provide a definition of an order of mammals). Second, some of these are either traits are probably primitive features of placental mammals or have arisen by convergence.

So, then how do we define primates?
Martin choose to examine living primates with an eye to creating a new definition, which I won’t bore you with since it is rather long.

You said the definition applies to living primates, what about fossils?
For fossils the definition has to be modified somewhat, but first we have to talk about tree-shrews.

?Tree-shrews?
Yes, you see Le Gros Clark argued that the Tupaiidae are more closely related to primates than to any other placental mammal and should be included in the order primates. This has been argued about ever since. Martin used tree-shrews as a test case for his definition of primates and decided (correctly, I think) that they were not primates.

That’s a pretty scientific approach!
Yes, it is. Paleoanthropology has a well developed scientific methodology and a rich body of theory to draw on.

So what about the fossils?
Since we have only skeletons to examine the definition has to be contracted somewhat. This is what is left:

Well developed, divergent hallux with flat terminal phalanx in the foot. Elongated distal segment of the calcaneus. Relatively large, convergent orbits with restricted interorbital distance. Postorbital bar present; ethmoid exposure in the orbit possible (depending in interorbital distance relative to skull size). Petrosal bulla. Relativly large braincase. Sylvian sulcus on endocast. Dental formula maximally 2.1.3.3/2.1.3.3. Premaxilla short; upper incisors arranged more trnsversly than longitudally. Molars with low, rounded cusps. Lower molars with raised, enlarged talonids.

So, does it identify fossil primates?
Yes, it does. According to this definition omomyids and adapids, for example, are primates.

What about plesiadapids?
The jury is still out on this issue.

Tomorrow: Omomyids, Adapids and Anthropoid Origins.

Intelligent Design and Human Evolution: Part II

Turning to the next section is like a breath of fresh air – even though it’s completely wrong at least it’s capable of being understood.

Limitations of Paleoanthropological Methods, Datasets, and Studies

In this sections Luskin purports to critique palaeoanthropology. He starts out with a quote by Gould to the effect that “most hominid fossils…are fragments of jaws and scraps of skulls” and Medawar to the effect that paleoanthopology is a humble and unexacting kind of science. Later in the section he claims that complete skulls are rare finds in paleaoanthropology. I suspect he is quote mining, but it really doesn’t matter, because he is still wrong. For example, a halfhearted attempt to count the number of fossils mentioned in Conroy’s Reconstructing Human Origins yielded over 2400 specimens, quite a few of which were complete skulls. I’ve encountered some estimates that put the total number in the tens of thousands – hardly fragments of jaws and scraps of skulls. In terms of methodology, palaeoanthropology draws on paleontology, geology, anatomy and evolutionary biology to name a few and has a rich, sophisticated theory base to draw on.

Luskin then claims that “A single skull…only provides one data point for an entire species and tells little about full ranges of morphological variation, extent sexual dimorphism and even the species true general form (whatever that is) through time. (pg 4)” At Omo over 500 specimens have been found representing gracile and robust australopithicines and early homo. At Sterkfontein over 600 specimens representing over 50 individuals from Australopithecus africanus, A. robustus and Homo habilis. At Makapansgat over 30 specimens representing approximately 12 individuals from A. robustus and H. erectus. At Hadar over 250 specimens representing approximately 35 individuals from A. afarensis. At Atapuerca/Gran Dolina 100 specimens from 6 individuals. At Atapuerca/Sima delos Huesos 28 individuals. At Predmosti 29 indicviduals. At Dolni Vestonce 35 individuals. At Krapina 800 specimens representing over 80 indivuals. At Vindija 80 specimens. At Skhul 10 individuals. At Shanidar 9 individuals. Whats missing from the list I just presented are sites such as Olduvai Gorge and Sangiran, among others. The amount of diversity in terms of morphology in the above list is certainly adequate to characterize the full range of variation for most of the species we are familiar with.

Coming soon: The Fossil Record of Non-Hominid Primates.

Chimps and Language: An Update

Carl Zimmer has someinteresting thoughts on chimps and language.

Intelligent Design and Human Evolution

Back in July of 2005 PCID published to articles on intelligent design and human evolution. One (Human Origins and intelligent design) was by Casey Luskin. The other (Reflections on Human Origins)is by Dembski. I will be examining both in a series of posts.

Both papers purport to offer the “Intelligent Design theory of human evolution. What they being, though, is a strange mix of creationist arguments and punctuated equilibria. I will start with Luskin.

Two Views of Origins

This section of Luskin’s paper lays out the differences between “blind natural processes” and ID. After a brief recapitulation of the paleoanthro version of human origins Luskin lays out the ID case. According to Luskin some proponets of ID argue there are limits to the amount of change in genetic information possible through “Darwinian processes” consequently, they have proposed a new taxonomic catagory. The new catagory is the “basic type” (where have I heard that before – oh wait from Gish, Morris and company). The basic type is defined as ” …a group of organisms related through ancestry that initially acquired their fundamental genetic programs through design, and not through ancestry with some other type of organism.” Luskin continues “Because their genetic architecture is distinct, members of one basic type cannot interbreed to produce offspring with members of another basic type. The converse is not necessarily true as some species which cannot interbreed could be members of the same basic type.” (pg. 2)

My first thought on reading this was “huh”. So I reread it several times. A new taxonomic catagory? Okay, where does it fit in the taxonomic scheme of things? Between species and genus, between genus and family? Between higher units? Better yet, why do we need another catagory? I still haven’t figured out what the next bit means. I understand a group of organisms related through ancestry… Then he threw a curve with …that initially acquired their fundamental genetic programs (though I don’t quite know what a fundamental gentic program is) not through ancestry with some other organism. So which is it? Are they related or not? Is this trying to say that, say prosimmians are a basic type in that they are related by ancestry but don’t share fundamental gentic prgrams with anthropoids. Oh well, skip that let’s move on. One basic type can’t interbreed with another because of different genteic architecture yet some species which cannot interbreed could be members of the same basic type? Then what good is the lack of inbreeding as a criteria for distinguishing basic types? I’m confused about this so let’s move on to how basic types appear in the fossil record and worry about definitions later. Apparently, basic types appear suddenly in the fossil record and will be different from previously existing critters. “This infusion of information could be revealed in the fossil record as a ‘quantum or discontinuous in specified complexity or information'”. I can’t help thinking they are stealing from Gould and Simpson here.

After laying this out, Luskin lays out the purpose of the paer, which is to test the hypothesis that some groups of “upper” primates were intelligently designed by looking at the fossil record and asking which groups belong to distinct basic types. So apparently, discovering a basic type is enough to justify the inference of intelligent design. Considering the tortured explanation of what a basic type is one thinks anything could be a basic type.

Coming soon: Limitations of Paleoanthropological Methods, Datasets and Studies.

Memery

Homework has been assigned by my blogfather so here it goes…

1. Of all the books that you have eventually finished after many starts & stops, which one took you the longest and how long did it eventually take?

Like PZ I choose “The Structure of Evolutionary Theory”. I started it about a month and a half ago – still working on it. Between the recent move (and all the packing) and frequent stops to think about what Gould is saying it’s taking a little longer than I anticipated. I beginning to fear I may have to start over to pick up the argument… It’s kind of like the “Song that Does Not End” on Lambchop. I think I’m doomed to endlessly read and reread it.

2. What great band (or album or song) have you heard so often, you wouldn?t mind never hearing again even though you still think the band (or album or song) is great?

That’s a toss up between “Free Bird” and “Simple Man” both by Skynyrd. I lived in the south for about six years and am sick unto death of these two songs…

3. Which cliché or often cited quote needs to be placed in quarantine for a few decades?

“Teach the Controversy” “Fair and Balanced” or maybe ” ______ (insert state name here) values” as in “My opponent doesn’t represent Missouri (or whatever) values”

4. During the 1990s “Compassion Fatigue” received a lot of press, now the media is giddy with “Donation Fatigue”. What will be the next trendy fatigue?

Missing White Girl Fatigue

5. What percentage of respondents will answer “meme fatigue” to question #4?

Fortunatley, I read PZ’s post and knew better than to answer Meme Fatigue.

I think I’ll pass this on to:

Oldwhitelady at It’s Morning Somewhere

Henry at Webiocosm

Aydin at Snail’s Tails

and

Duane at Abnormal Interests

Oh, and let me just point out that we Spawn of Pharyngula moved out in the blogosphere so we didn’t have to tidy our rooms or do homework!

"Junk" DNA and Fruit Flies

Added 11/2/05: Welcome visitors from Evolgen. Make yourselves at home, feel free to look around and if you like what you see do come back! I should mention I agree with Evolgen that “Junk DNA” is a term that should be dispensed with.

Genetics is an interesting, if mind numbingly complicated, subject. As you all know genes are composed of four nucleotides that form pair bonds with each other (to be simplistic). Adenine pairs with thymine and guanine pairs with cytosine. Three base pairs form a codon, etc. Traditionally, a gene is defined as a segment (i.e. series of codons) that code for a polypeptide chain or specifies a functional RNA molecule. This brings us to repetitive DNA. Repetitive DNA consists of nucleotide sequences that occur several times, either in tandem or are dispersed. For example, the genome of the kangaroo rat contains over 50% repetitive DNA in the form of three, localized, repeated sequences. These are AAG, TTAGGG and ACACAGCGGG. Each sequence is repeated from one-two billion times. Another type of repetitive DNA is dispersed throughout the genome and are divided into two major types: short interspersed repeated sequences and long interspersed repeated sequences (of which their is only one in the human genome). A number of mechanisms have been suggested for the creation of repetitive DNA including gene duplication, transposition, unequal crossing-over and replication slippage. The problem is, however, what function the repetitive sequences serve. Four possibilities have been suggested:
1) They perform essential functions, such as global regulation of gene expression. This implies that removal of repetitive DNA will have a deleterious effect.
2) Repetitive DNA is useless “junk” DNA and it’s loss will have no effect of fitness.
3) It is a fucntionless parasite
4) It has a structural function unrelated to carrying genetic information. For example, it may affect chromosomal architecture such as curvature.

Recently, a study was done which seems to support the first possibility. Here is a little more background:

“Sequencing of the complete genome in humans, fruit flies, nematodes and plants has revealed that the number of protein-coding genes is much more similar among these species than expected,” he says. “Curiously, the largest differences between major species groups appear to be the amount of ‘junk’ DNA rather than the number of genes.”

Using a recently developed population genetic approach, Andolfatto showed in his study that these expansive regions of “junk” DNA—which in Drosophila accounts for about 80 percent of the fly’s total genome—are evolving more slowly than expected due to natural selection pressures on the non-protein-coding DNA to remain the same over time.

“This pattern most likely reflects resistance to the incorporation of new mutations,” he says. “In fact, 40 to 70 percent of new mutations that arise in non-coding DNA fail to be incorporated by this species, which suggests that these non-protein-coding regions are not ‘junk,’ but are somehow functionally important to the organism.”

The research found that a large amount of the functional divergence between Drosophila species was exhibited in the “junk” regions.

(The info on repetitive sequeces came from Li and Graur’s 1991 book “Fundamentals of Molecular Evolution”)

From the Mouths of Babes – Well Teenagers Really

So, the afarensis family is watching the news and they are talking about yesterday’s suicide bombing in Iraq and the youngest afarensis offspring says “Ya know, this has been going on for several years. I don’t know who we are fighting and what we are fighting for, I’m so confused.” Pretty much summed it up.

How Fossils are Made

Blog Lineages

Pharyngula mentions that The Politburo Diktat is trying to trace blog lineages – who inspired who to start blogging. Here are the questions to answer – leave a comment at his place:

1) Blogfather or Blogmother (Just one): Pharyngula – I had been a lurker and PZ made explaining biology concepts look sooo easy, I decided I could do it to. To my intense shock, it’s not as easy as he made it look!

2)Blog Birth Month: 10/2/04 4:50 AM.

3)Blog Spawn (have you inspired anyone to start blogging?): Alas, no! I would never, I’m not that kind of hominid! Well, okay, not to my knowledge – but if I have inspired you to start blogging let me know.