Yet More on New World Origins

According to this article in Science Daily. Humans arrived in america 12,000-14,000 years ago. The interesting part is how the estimate was determined.

“The estimated effective size of the founding population for the New World is about 70 individuals,” Hey said. “Calculations also showed that this represents approximately 1 percent of the effective size of the estimated ancestral Asian population.”

“Effective size” in population genetics is often thought of as the number of adults of reproductive age. One rule of thumb is the effective size might be about one third of the ‘census population size’ which, in this case, comes out to about 200 people.

In addition to population size, Hey’s rigorous and complex methodology also generated historical estimates of when the divergence occurred. His dates are consistent with much of the archaeological record — in the range of 12,000-14,000 years ago.

The full article will be published in the June edition of PLoS Biology. I can hardly wait!

Biology and Machines: Part II

Intelligent Design advocates like to make an analogy between cellular processes and machines. For example Behe says:

And in the past 50 years, science has discovered that at the very foundation of life there are sophisticated molecular machines, which do the work in the cell. I mean, literally, there are real machines inside everybody’s cells and this is what they are called by all biologists who work in the field, molecular machines. They’re little trucks and busses that run around the cell that takes supplies from one end of the cell to the other. They’re little traffic signals to regulate the flow. They’re sign posts to tell them when they get to the right destination. They’re little outboard motors that allow some cells to swim. If you look at the parts of these, they’re remarkably like the machineries that we use in our everyday world.
The argument is that we know from experience that machinery in our everyday world that we use in our everyday world required design, required an intelligent agent that put it together, who understood how it was going to be used and who assembled the parts. By an inductive argument, when we find such sophisticated machinery in other places too, we can conclude that it also requires design. So now that we found it in life and in the very foundation of life, I and other ID advocates argue that there is no reason to not reach the same conclusion and that in fact, these things were indeed designed.

Actually the correct conclusion would be that since all the machines we are familiar with were designed by humans, cellular machines were designed by humans as well – but note the shifting language of the premise.

Also here Behe says:

In many biological structures proteins are simply components of larger molecular machines. Like the picture tube, wires, metal bolts and screws that comprise a television set, many proteins are part of structures that only function when virtually all of the components have been assembled.

And here is Calvert:

We intuitively infer design when we observe the awesome complexity of the living information processing systems that comprise life. When we look into the black box of the cell we see a biological language, input devices, application programs, information processors, output devices, and systems designed to collect and process energy, make decisions and direct the construction, maintenance and operation of cellular machines and systems. DNA is a blue print that has a semantic or meaningful characteristic found in any writing produced by a mind. That semantic characteristic has not been explained by natural law and chance. Non-natural machines and information processing systems are the kinds of effects that are produced only by human minds. Hence, analogy leads to a reasonable inference that intelligence may also be the cause of similar biological machines and information processing systems.

So, how acurate is the analogy? Let’s look at protein synthesis. Before proceeding, however, let me mention that the following synopsis is drawn from Genes VI by Benjamin Lewin and Molecular Biology of the Cell by Alberts et al. Any mistakes (and I hope there are few) are mine.

Ribosomes Posted by Hello

Anyone who has had biology knows the process (the picture above is a graphic overview of the process). The DNA helix unwinds, the mRNA makes a complementary template, ribosomes bind to the mRNA strand and tRNA brings the amino acids that will form the protein. This is the way it is usually presented (with a little more detail) and it all sounds very straight forward and machine like. In reality, there is a lot more to the process than that. In bacteria free RNA polymerase collide randomly with DNA , with most sticking very weakly to the DNA. When the RNA polymerase hits the promotor region, however, it binds tightly and transcription begins (which in and of itself is a good argument against the whole notion of irreducible complexity – which is related to the machine analogy).
In eucaryotic cells (cells with a nucleus) the transcription part of the process occurs in the nucleus. The DNA strands are opened by an RNA polymerase which exposes a short section of nucleotides (I’m still simplifying greatly) . The RNA polymerase then binds incoming ribonucleoside triphosphate monomers to form a chain. Once a RNA chain is completed it moves out in the cytoplasm for the translation process. It is here where I really want to pick up the story in more detail.
In order for the translation process to occur the mRNA molecule has to be unwound and there are several factors ( called, in eucaryotic cells, eIF-4, eIF-4A and eIF-4B) that actually start unwinding the mRNA molecule at the 5′ end.

mRNA Posted by Hello

Ribosomes then attach to the 5′ end and migrate towards the initiator codon – a sequence of the three bases AUG. The distance between the 5′ end and the initiator codon varies between 50 and 1000 bases (imagine if the timing chain on your car displayed similar variation in where it was set – while the car was running, would it still run?). As it moves down the mRNA the ribosome occasionally encounters obstacles – called secondary structure hairpins – that prevent it from moving further. At that point the ribosome disassociates into it’s two smaller subunits and the process starts over again (imagine if you car had a blocked gas line – could it over come that and continue running?). The optimum start sequence is GCCA/GCAUGG. The A or G three sequences before the start codon and the G immediately after are particularly important, they increase the efficiency of translation by a factor of 10 (which would be like having a car that got 10 mpg when you put regular in it but 100 mpg when you put unleaded).

tRNA Cloverleaf Posted by Hello

Okay, we have the ribosome at the initiator sequence. What happens next? Well, the initiator sequence (AUG) actually codes for methionine and two different types of tRNA can carry it. One type of tRNA is used in initiation and one type is used in elongation. If you look at the picture above at the top of the picture (labeled acceptor region) the initiator would read ACCA-met-formyl. The anti-codon arm would have 3 G-C pairs in the stem. This is where things really get interesting. Although I mentioned above that the initiator site is AUG, the initiator tRNA can also recognize GUG and UUG. The kicker is that when GUG is used elongation efficiency is reduced by half and when UUG is used elongation is reduced by half again (it would be like if your car ran okay when gas was used as fuel, half as well if beer was used and a quarter as well if water was used – but your car don’t work like that does it?). The process is even more variable (that’s an important word I will get back to later). I mentioned above that the initiator tRNA has a formyl group on it, but this is actually not necessary, but it does increase the efficiency with which tRNA is bound by a factor (IF-2 for those that know a lot about this) that aids the process. One final wrinkle before I proceed to a description of the process itself. The last two bases in the acceptor stem of the initiator tRNA are unpaired. This prevents the initiator tRNA from being used in elongation. Mutations, however, frequently occur which create a base pair in this position and allow it to function in elongation (in my opinion this undermines everthing Dembski is arguing for and the whole notion of irreducible complexity – but I’m not a biologist so I could be wrong).

Translation Posted by Hello

So, shall we build a protein? The top portion of the above picture shows a mRNA strand with an intact ribosome. This is about half a step ahead of where we need to be. Ribosomes are composed of two units – a small and a large which exist in a pool of free ribosomes. Initiation of synthesis is undertaken by the separate subunits. The small subunit binds to the the mRNA and travels to the initiator region. At this point the P-site (see picture above) on the ribosome lies over the initiator region on the mRNA strand forming an initiation complex. The only tRNA that can join the complex, at this point, is the initiator tRNA. The larger subunit joins the complex and makes the A-site available for a tRNA complementary to the second codon on the mRNA. This also is quite variable. Sometimes the process stalls and the the subunits and tRNA are released and the process starts over. Assuming it continues, the tRNA in the P-site transfers it’s product to the tRNA in the A-site and the ribosome moves forward one codon. This moves the tRNA in the A-site to the P-site making room for another tRNA in the A-site. The previous occupant of the P-site is released via a third site on the ribosome called the e-site. Here again, there is some variability. Sometimes the wrong tRNA enters the A-site, binds temporarily and is released. Ocassionally, a tRNA enters the A-site with four codons instead of the normal three. Most of the time it is released but occasionally, it’s product is incorporated into the protein. At any rate, the ribosome travels down the mRNA strand until it reaches the termination codon, at which point the finished protein is released and the ribosome is released back into the pool. The mRNA usually has more than one ribosome traveling down it and after a while degrades.
The picute below is the real thing. In the bottom portion you can see ribosomes (the round things) traveling down a mRNA strand. Sticking out of the ribosomes are long strings – which are actually proteins in the making ( I don’t see any machines, do you?)

Elongation Posted by Hello

Summing things up, protein synthesis is a variable process. There are approximately 20,000 ribosomes in cell (and they compose 1/4th of the cell mass). There are approximately 3000 copies of each tRNA as well as 1500 mRNA’s in various states of synthesis and decomposition. They all exist in a dynamic equilibrium. To quote Tom Misteli:

“No longer can we think of cellular machines as stable, static, and precisely-assembled complexes, akin to man-made machines.”

Instead, researchers found that polymerase subunits came together and formed a complex each time a gene was read, on average every 1.4 seconds. Computer simulations suggest that each formation resulted from random, chaotic interactions between protein subunits that eventually came together in the proper configuration. (emphasis mine) Once a complete polymerase finished reading a gene, the subunits quickly disassembled and scattered throughout the cell. Researchers speculate that the dynamic nature of cellular machines allows components to assemble as needed in response to changing environmental conditions.

All through this post I frequently made comparisons to cars. The point was that designed objects are characterized by their lack of tolerance for variability. I recently put together a book shelf. Problem was, apparently, the manufacturers drill press was out of alignment so the bolt holes didn’t match. Which meant I couldn’t put the shelf together and so it was completely useless as a book shelf. Cars, motors, planes – anything made by human hands show the same characteristics. Change the operating environment they were designed for (the chronic problems of military hardware in Iraq is a good example) and they rapidly break down. We do not see these qualities in nature though. During protein synthesis any number of things can and do go wrong yet the process continues (it goes without saying that the ability to overcome variability. Phrased another way, biological processes adapt to variability in their environment, designed things don’t.

Coming Soon: Part III Semantics and Logic

Biology and Machines: Part I

Regular readers of this blog are no doubt aware that ocassionally have a few things to say about intelligent design/creationism. Particularly in regards to the analogy intelligent design advocates make between cells and machines. Here for example. I have been doing research on this with an eye to writing a post examining how well the analogy holds up in protein synthesis (which I mentioned earlier in the week. In the blogosphere, if you procrastinate you get pre-empted. In this case Pharyngula has written an excellent post on the analogy between genes and machines. Normally, when I come across a post similar to one I am thinking about I usually scrap the idea (seems too me too-ish to continue). Especially if the writer says pretty much everything I was planning on saying. After reading PZ Myers post I decided to proceed with mine since I am approaching the issue from a somewhat different angle.

A Change of Pace

You may have noticed a section in my links called “Here There be Monsters…” I am actually quite addicted to Monster Movies. I prefer the older ones especially anything staring Boris Karloff, Lon Chaney Jr or Bela Lugosi. I also like anything with Chris Lee (last seen as Saruman)or Peter Cushing (last seen as Darth Vader’s right hand man Grand Moff Tarkin) – anything with Godzilla in it is also good.
I bring this up because yesterday I watched all three Jurassic Park movies and had a couple of thoughts on them – the fact that I just did a longish post on Stegosaurs also factored into it.
There is a tradition in horror movies dating back to 1925’s The Lost World to portray dinosaurs as nothing but killing machines wandering from one killed beast to the next with nary a pause for dinner.
Lost World 1925 Posted by Hello

King Kong continued the tradition. While they are still on Skull Island Kong has to fight off any number of dinosaurs. There is also the scene with the Stegosaurus and the scene with the bronto – umm – apatosaurus (where a large majority of the crew are killed).

King Kong 1933 Posted by Hello

Valley of the Gwanji , made in 1969, continued the trend. Gwanji (I have never quite made up my mind whether it was supposed to be a T-rex or an allosaurus) roamed the valley indiscriminately killing anything that moved.

Valley of the Gwanji 1969 Posted by Hello

In some ways the Jurassic Park movies are a continuation of this trend. Granted the herbivorous dinosaurs are portrayed somewhat realistically, but the carnivores still kill anything that moves – even if it just ate.

Intelligent Design and the Evolution of the Eye

As part of their response to Dawkins, ID the Future has the following post Dawkin’s Eye-con of Evolution Unravels. It’s pretty pathetic really.

Dawkin’s says:

“The eye is today a showpiece of the gradual, cumulative evolution of an almost perfect illusion of design. The relevant chapter of my Climbing Mount Improbable is called ‘The fortyfold Path to Enlightenment’ in honour of the fact that, far from being difficult to evolve, the eye has evolved at least 40 times independently around the animal kingdom.”

The Response:

Only someone who does not know, or does not care to know, the myriad problems with eye evolution could make such a claim with a straight face.

Then they provide a link to Belinski totally distorting and misunderstanding research published in the Proceedings of the Royal Society of London. This whole issue has been addressed elswhere.

I would just like to recommend that the folks over at ID the Future read the following three books:

Evolution above the Species Level, B. Rensch
Vertbrate Eye and It’s Adaptive Radiation, G. Walls
Visual System in Vertebrates, Crescikilli

They will straighten you out on all those areas on the evolution of the eye that are confusing you. You might also want to reread the first paragraph of Dawkin’s article.

Is afarensis Going Senile?

Really, totally forgot to supply some interesting Dinosaur links I found while working on the previous post. Been doing that a lot lately. Forgot about the Friday Ark again (two weeks in a row, no less)! So here they are:


Some Interesting Lecture Notes

Dinosauria Online

DinoData Home Page

(I’ll be adding this one to my blog roll – along with a few others when I get time)

Added a few minutes later: I will definately be adding Palaeoblog to my blog roll – dudes got some excellent journal links, wonder if he will let me steal them for the Evil Darwinian Orthodoxy? Which, let me say, I am always on the look out for more journals (hint, hint).

Stegosaur Plates and Intelligent Design

Stegosaur Skeleton Posted by Hello

This and this is really interesting.
Stegosaurs roamed the earth from the Middle Jurassic to the Late Cretaceous. They are related to ankylosaurs and form a larger grouping (the Thyreophora) with them in the order Ornithischia (named after the shape of the ischium). Stegosaurs are one of the more popular dinosaurs and have been used in movied such as “Fantasia” and “Jurassic Park II:The Lost World” One of the reasons, perhaps the only reason, for their popularity is the series of plates running down their back and ending in four massive spikes on thier tail (used to incredibly dramatic effect in Fantasia). Paleontologists have always been somewhat puzzled as to what these plates were for. There are four theories to explain these plates.

2)Heat Regulation
3)Sexual Selection
4)Species Identification

A study to be published in the upcoming issue of the journal Paleobiology examines these exlanations and concludes that number four is probably correct. The study is authored by Paidan, Main, Horner and de Ricqles.
They examined the histology of the plates and scutes of stegosaurs and their relatives (the Ankylosaurs and Scutellosaurus among others).
They ruled out the use of the plates as a defense mechanism because they are very thin and only lie along two rows on the back – which doesn’t provide that much protection (especially when the amount of energy required to grow them). They also ruled out the role of sexual selection because female stegosaurs had the plates too – so they couldn’t be the result of male-male competition or female choice.

Stegosaurus Plate Posted by Hello

This leaves thermoregulation and species identification as possible explanations. Stegosaur plates have large blood vessals leading into them, and, as mentioned above, are extremely thin. This has lead to the idea that they are involved with heat exchange with the environment (as are, for example, the ears of elephants and the flippers and tails of seals). From the press release:

As for heat exchange, one major reason earlier scientists proposed such a function for stegosaur plates is that these plates have large blood vessels piercing their interior, perhaps channels to carry blood to be cooled or heated. But it turns out that these “pipes” lead to dead ends, so their roles as major blood vessels are difficult to establish.

To probe the possibility that the plates and spikes were heat exchangers, the paleontologists looked at the evolution of these skin growths in the thyreophoran family, which included the stegosaurs. The team obtained fossils from a half-dozen different species of thyreophorans, ranging from the stegosaurs’ earliest ancestors – “armored” dinosaurs that lived 200 million years ago – to the first stegosaurs and related ankylosaurs – which had bony plates or scutes all over their bodies – to the last stegosaurs, which died out in the Early Cretaceous period more than 120 million years ago. All were plant eaters with formidable flat or erect plates on the neck, back and tail. The team sliced through about 10 fossil scutes to study their internal structure.
Added a few days later: Here is an example of one of the thin sections.

Stegosaurus Plate Posted by Hello

The earliest thyreophorans, such as the North American dinosaur Scutellosaurus, which measured about four feet from nose to tail, had small bony plates lying flat over their backs and tails, each with a slightly raised keel. These scutes, about a half-inch across, had an internal structure similar in some aspects to the much larger plates of the stegosaurs, yet were obviously useless in regulating the internal temperature of the animal, Main said. The same is true of the later Scelidosaurus, a 13-footer covered with larger scutes with bigger keels; the scutes had the same type of blood vasculature as stegosaur plates and spikes. Ankylosaurs, a sister group to the stegosaurs that survived into the late Cretaceous and went extinct with the rest of the dinosaurs 65 million years ago, had more diverse scutes and ossicles that nevertheless were plumbed in the same way as those on stegosaurs.

Based on this analysis, the team argued that it was unlikely that the larger plates that evolved in the stegosaur ancestors of Scutellosaurus and Scelidosaurus were used for heat exchange.

Below is a picture of the skeleton of a species related to stegosaurus – called Huayangosaurus. It was found in China and is from the Middle Jurassic. Note that it has small plates intermixed with spines. Paidan et al are argueing that becuase Huayangosaurus and Stegosaurus were related their plates and spikes would have come from a common ancestor and would serve roughly the same purpose. If that purpose was thermoregulation they would be a lot similar than what they are.

Padian and Main point out, too, that the horns or antlers of many living animals contain large vessels to supply blood needed for fast growth. None of these horns or antlers function as heat exchangers. A possible role of the large “pipes” in the scutes of stegosaurs and their ancestors was to carry the large blood supply needed for the fast growth that was thought to be typical of dinosaurs.

In addition, not all stegosaurs living at the end of the Jurassic had the big, flat plates of Stegosaurus stenops that most people associate with stegosaurs. Kentrosaurus of Africa and the Asian Huayangosaurus, which were about the same size as Stegosaurus, had mostly spikes with a few “dinky” plates, Main said. These spikes and small plates would have been useless for heat exchange.

“You get quite a large variety in the types of osteoderm arrangements in these animals, but they are not specialized in the way that one would expect if they were built specifically for a thermoregulatory function,” he said. “What it looks like is the scutes simply show hypertrophic growth of the keel region, it’s simply a modification of an already existing growth pattern.”

Huayangosaurus Posted by Hello

This leaves us with species identification as the explanation:

“There is a natural tendency that leads to elaborate displays for social group recognition, like the calls of birds,” Padian said. “This underscores the importance of behavior to evolution.”

And from National Geographic News:

“The skeletons of these dinosaurs [stegosaurs] below the neck are identical,” Horner said. He points to deer as a modern-day analog: While the skeletons of mule deer and white-tailed deer look very similar, the animals themselves have different colors, and their ears and tails are also different.

Horner says these deer attributes serve a similar function to that of the elaborate frills, crests, and back spikes found in dinosaurs. They allow mule and white-tailed deer to identify members of their own species.

Referring to the dinosaurs, Horner noted that “all of these big features on dinosaurs are very expensive” in terms of the energy required to grow them. He added that such features must therefore be extremely important.

At this point, three out of four hypothesis’ concerning the function of stegosaur plates have been eliminated. Some of the evidence suggests that the fourth (species recognition) may be correct. A note of caution, however:

De Ricqlès cautioned, however, that “an accessory role in thermoregulation cannot be ruled out for the Stegosaurus plates. Being so large, well vascularized (and available) they may have been inevitably exapted for such a function. This is so even if the primary explanation of their occurrence in an evolutionary context may be elsewhere: namely in some sort of ‘display’ (mate or species recognition), as suggested by the comparative, phylogenetic, context of plates development among Stegosauria.”

So how do we proceed? Let’s ask for a few outside opinions. What’s your advice William Dembski?:

But is the problem ignorance of the material causes needed to bring about biological complexity or an inherent inability of such causes to do so?

So, we should just infer intelligent design and call it a day.
Richard Dawkins what is your advice?

Science mines ignorance.
Mystery – that which we don’t yet know; that
which we don’t yet understand – is the mother lode
that scientists seek out. Mystics exult in mystery
and want it to stay mysterious. Scientists exult in
mystery for a very different reason: it gives them
something to do. Maybe we don’t understand yet,
but we’re working on it! Each mystery solved
opens up vistas of unsolved problems, and the scientist
eagerly moves in.

So we have two different opinions. One says stop, enjoy blissful ignorance and say God did it. The other says don’t despair, accept the unknown as a challenge and go forth to meet it.

To investigate further whether the elaborate horny displays of stegosaurs and other dinosaurs are involved in sexual displays, Padian is going to South Africa in May and June to measure skulls and bodies of African antelopes to look at the range of sexual dimorphism. Such studies have never been done on a full range of African bovids, he noted. Meanwhile, Main at Harvard is studying bone growth and skeletal mechanics in animals such as goats and emus to see how they change with age.

“We know more about growth in some dinosaurs than we do about growth in large living mammals,” Padian said.

Looks like Dawkins wins! A wonderful example of how science operates!