New Find Challenges Evolution

I've been a passionate supporter of evolution, but now . . .

A recent find from the Flinders Ranges of South Australia will shake the theory of evolution to the core. But no-one knows about it.

Why?

I've tried to talk to palaeontologists about it, but the refuse to discuss it. Evolutionists I've known for years no longer reply to my emails. I've been ignored buy organising committees for conferences and symposiums in favour of other evolutionists when I have earth shattering evidence against their pet theory.

They may have frozen me out, but I will not be silenced.

From a Precambrian site deep in the Flinders Ranges, I was guides by something . . . or someone, and I found startling remains - reptile remains with clear preservation of skin. How could that be if the 'so called' (in my opinion now) theory of evolution is true? How can exceptionally preserved reptile remains be present at a Precambrian site?

It can't. But it is. So evolution must be false.

Click on the link below and spread the evidence the the evolutionists have tried to stop me from exposing.

Reptiles in the Precambrian disproves evolution

Evolution Among the Trilobites - Part 2

Meet the family. Estaingia (right) and Xystridura (left).
In Part 1 we looked at the growth patterns of the Early Cambrian trilobite Estaingia bilobata, using certain measurements from the head, or cranidium. In this part we'll compare and contrast those growth patterns with the Early Cambrian trilobite Xystridura templetonensis. You can click on any of the images and graphs to get a larger version.

The change through time in the appearance or rate of development of ancestral characters is known as Heterochrony, which comprises two basic phenomena (pay attention, there'll be a quiz at the end!):

Paedomorphosis - the retention of ancestral juvenile characteristics in a descendant adult. Paedomorphic forms usually pass through fewer morphological stages during growth than their ancestors (in other words less time as a juvenile you stop being a juvenile early, before you've shed all the baby characters). There are three types of peadomorphosis

Deceleration - the rate of morphological development is reduced during the juvenile phase (slower development, but the same amount of time is spent as a juvenile, so the same size as the ancestor, but you have not completed the juvenile development so have a baby-faced adult)
Hypomorphosis - the onset of maturity occurs at an earlier stage of development (same development but less time as a juvenile, so a smaller adult then the ancestor - still baby-faced though).
Post-displacement - a change in the timing of the onset of certain features, with one or more structures starting to develop at a later stage (the same amount of time is spent as a juvenile, so the same size as the ancestor, but the structures are smaller in the adult)

Peramorphosis - the appearance of ancestral adult features in the descendant juvenile stage (beards on a baby!). Here to there are three processes:

Acceleration - increasing the rate of morphological development (if maturity is also accelerated then adult will be smaller then the ancestral adult, if the onset of maturity is not affected, the the adult will be the same size as the ancestral adult).
Hypermorphosis - delayed maturity so the juvenile stage is extended (spend longer as a juvenile, so the adult is bigger)
Pre-displacement development of structures occurs at an earlier stage of development (same time as a juvenile, but structures more developed and bigger).

Before we look at a comparison between Estaingia and Xystridura, lets refresh what it is we are actually measuring (see Estaingiacranidium (or head) at right). The relevant measurements that we are interested in are; Cranidial Width (CW), which is literally the distance between the eyes; the Pre-glabella Field (PGF), which is the area in front of the large bulbous glabella (incidentally the pre-glabella field only runs to the shallow trench towards the front of the cranidium. In front of the trench is the doublure. That is folded underneath the cranidium in life, along the trench, and pops up during moulting); Glabella Length (GL), adding PGF and GL gives us a value for the length of the cranidium; Pre-Orbital Glabella (POG), which is the bit of the glabella that lies in front of a line drawn between the front tip of the eyes; and the distance between the end of the Axial (or Occipital) Furrow (the trench behind the glabella) and the back tip of the Eye Lobe (AF-EL). (Note that the figure is missing the free cheeks. This is because they are usually lost or repositioned during moulting. Trying to measure missing of displaced portion of the head would not allow accurate measurements. The measurements here, therefore, are all done on cranidia (without free cheeks).

The story is that Xystridura (Middle Cambrian) has evolved from Estaingia as represented by forms from the Emu Bay Shale (Lower Cambrian) through changes in the rate of development of certain characters, or hererochrony.

Now, to look at changes over time we will be comparing ratios, not individual characters. Individual characters will usually grow over time, but we are interested in how that character changes with growth. If the character increased with growth at a greater rate than other characters, then the ratio increases. If the character increases with growth at a lesser rate than other characters, then the ratio decreases. If the character increases at the same rate as other characters then there is no change in the ratio.

The first character we will look at is the distance between the back of the eye and the occipital furrow (AF-EL).

Measurements of meraspid Estaingia and Xystridura.
Xystridura measurements adapted from McNamara (1981).

Here, the ratio AF-EL/CL compared with cranidial length is plotted with growth (cranidial length is taken as a proxy for growth) for meraspid (juvenile) Estaingia (yellow) and Xystridura (black). Here the smallest (youngest) meraspids have the largest ratio, and as they grow that ratio decreases. This means that, with growth, the feature is increasing at a slower rate than the overall growth rate. We can also see that Estaingia and Xystridura plot together. This means that the juvenile growth pattern is the same for both. The big difference is that the Xystridura meraspids continue beyond the transition from Estaingia meraspid to holaspid (adult) (yellow dotted line). The Xystridura meraspid to holaspid transition (black dotted line) occurs later than Estaingia and so Xystridura meraspids grow to a larger size before the holaspid stage than do Estaingia meraspids. So the onset of maturity is delayed and the juvenile growth phase has been extended.

The largest Xystridura meraspid appear to have a smaller AF-EL/CL ratio than Estaingia meraspids, but the spread of data is large.

Obviously, the character itself - the distance between the back of the eye ridge and the occipital furrow - increases throughout growth in absolute terms, but that increase is at a slower rate that the overall growth of other characters, so the ratio decreases.

No lets look at what happens during holaspid growth.

Measurements of Estaingia and Xystridura.
Xystridura measurements adapted from McNamara (1981).

The first thing to note is that the meraspid growth pattern of reducing AF-EL/CL ratio is halted at the meraspid-holaspid transition. In the holaspid growth phase the AF-EL/CL ratio does not change with growth, which means that it is now increasing at the same rate as the length of the head. Also the spread of data at the meraspid-holaspid transition for Xystridura meraspid settles down in the holaspids suggesting that the timing of the transition has a bit of slop in it.

The second thing to note is that Estaingia and Xystridura have the same growth pattern - exactly the same growth pattern. Having a similar growth pattern could be chance - maybe this is a common growth pattern for trilobites. But having exactly the same ratio values is unlikely to occur by chance. This is strong evidence of an evolutionary relationship. Xystridura has inherited this particular ratio pattern and values from Estaingia.

Note also the "NSW Estaingia". This is Estaingia bilobata from Cymbric Vale in New South Wales. It is slightly younger than the Estaingia bilobata from the Emu Bay Shale. There are few measurements, but this form plots on the same trend and ratio values as the others - albeit a larger form than the Estaingia bilobata from the Emu Bay Shale.

Lets look at another character, this time the ratio of width compared with length of the head CW/CL

Measurements of meraspid Estaingia and Xystridura.
Xystridura measurements adapted from McNamara (1981).

Here again are the meraspid measurements for Estaingia and Xystridura. Again the character ratio decreases with growth. This means that as the head grows, the width is growing at a slower rate than the length. Also, the Xystridura meraspid growth phase is extended. This time however, there does seem to be some difference between the Estaingia and Xystridura meraspid growth phases. Unlike the last example, where the two growth patterns seemed to be in step. here the Xystridura meraspids appear to change the growth pattern. The larger Xystridura meraspids appear to stop the trend of decreasing CW/CL ratio and, by the time they reach the meraspid-holaspid transition, they appear to be slightly increasing the CW/CL ratio.

Things should become clearer when we look at the complete growth patterns.

Measurements of Estaingia and Xystridura.
Xystridura measurements adapted from McNamara (1981).

Here the growth patterns are markedly different. It should be pointed out that holaspid growth changes usually occur at slower rates than for meraspid forms, so that holaspid trends are less marked than meraspid trends. The Estaingia growth pattern shows that the reduction in the CW/CL ratio occurring in the meraspid growth phase is slowed at the meraspid-holaspid boundary. In the holsapid growth phase, the growth pattern shows that cranidial width continues to grow at a slower rate than cranidial length, but the difference between the growth rates is reduced somewhat.

However, for Xystridura, the apparent change in growth rate that occurs in the latest meraspids is carried into the holaspid growth phase, where the CW/CL ratio not only equalises (that is the width is growing at the same rate as length) but the width growth rate actually appears to be slightly exceeding the length growth rate.

Critically this change in Xystridura growth pattern occurs in the meraspid phase, but at the point where Estaingia would be expected to transition into the holaspid growth pattern. It isn't very clear in the graph (so click on it to enlarge) but the new growth pattern of the larger Xystridura meraspid after the Estaingia meraspid-holaspid transition (yellow dotted line) shows that the width is actually growing faster than the length (CW/CL ratio is increasing). At the Xystridura meraspid-holaspid transition (black dotted line) this growth rate actually slows down so that the width growth rate only slightly exceeds the length growth rate.

The NSW Estaingia actually plots between the Estaingia and Xystridura, suggesting that this change was underway by the time of Cymbric Vale sediments deposition.

The one thing that controls the cranidial width is the large bulbous thing in the centre of the head - the glabella. What these measurements are telling us is that during Estaingia meraspid growth, the glabella increases in width at a slower rate the the increase in the length of the head. During holaspid growth, the rate of growth of glabella width actually increases, but still not to the rate of increase of the length of the head - the glabella has increased the pace of its growth, but not enough to match the rate of growth in length the head is achieving - resulting in a slowing of the trend that is reducing the ratio of width to length, but not enough to stop the trend. In Xystridura, the glabella width actually starts to grow at a faster rate than the length - it is increasing in width ata faster rate than the head is growing longer - and so the ratio starts to increase.

If the glabella is changing size in one direction, maybe it's changing in another. Lets see.

The length of the head is composed of two measurements, the glabella. and the field in front of the glabella - the Preglabella Field (PGF) Any change in the glabella will affect the PGF. If the glabella increases in size at a faster rate than the length of the cranidium, then the PGF will reduce, if the glabella increases in size at a slower rate than the length of the cranidium, then the PGF will increase. If the glabella increase in size at the same rate as the length of the cranidium, then the PGF will remain the same. Measuring the PGF then, provides a proxy for glabella length growth.

Measurements of meraspid Estaingia and Xystridura.
Xystridura measurements adapted from McNamara (1981).

For Estaingia meraspid, the PGF is increasing with increasing meraspid size. This means that the glabella is growing at a slower rate then the length of the head resulting in an expanded PGF. By the Estaingia meraspid-holaspid transition, this pattern has stopped.

The Xystridura meraspid growth pattern follows the Estaingia meraspid pattern in showing an increase in the size of the PGF up to a certain point. Then, just before the Estaingia meraspid-holaspid transition this trend reverses, and the PGF reduced in size. This means that the glabella is now increasing in size at a greater rate than the length of the cranidium, resulting in a reduction in the PGF.

What does that mean for the holaspids?

Measurements of Estaingia and Xystridura.
Xystridura measurements adapted from McNamara (1981).

Lets take Estaingia first. After the meraspid-holaspid transition, the PGF ratio decreases slowly. This indicated that the glabella is growing at a faster rate than the cranidial length, so the PGF is getting smaller, but only slowly.

After the Xystridura meraspid-holaspid transition, Xystridura shows the same pattern of slowly reducing PGF and so slowly increasing glabella. But, as the Xystridura meraspid phase lasted longer, the trend to reducing PGF (increasing glabella) starts in the meraspid period and is accentuated. So much so that, by the time of the Xystridura meraspid-holaspid transition, the PGF is so small that even at the slowly reducing rate of the holaspid form, the PGF reached zero shortly after the Xystridura meraspid-holaspid transition. This means that the the glabella has been growing at such a faster rate than the cranidium, that it is so close to the front of the cranidium by the time of the meraspid-holaspid transition, that it quickly reaches the front of the cranidium early in the holaspid phase. PGF = 0.

Interestingly, the NSW Estaingia plot with the other Estaingia. This indicated that this change had not yet started by Cymbric Vale time.

All it took to produce a descendant form that looks significantly different from the ancestral form is the simple process of slightly delaying the onset of the holaspid phase, resulting in some of the slower holaspid growth pattern being incorporated into the faster meraspid pattern. In other words the large bulbous glabella of Xystridura is caused by a portion of the holaspid growth pattern being incorporated into the meraspid growth phase. "But wait a minute", you say (or you would say if you were paying attention) "the first character didn't change at all, and that involves the glabella - it measures the distance between the back of the eye ridge and the side of the back end of the glabella". That's true, but the growth of the glabella is focused towards the front of it. It is the front portion that has grown, not the back portion. So the back remains unaffected by the change.

Why is the glabella important? Well, that's where trilobites keep the stomach. So big glabella, big stomach.

So, what type of heterochrony is this? Go back to the list at the start and work it out.






I'll give you a clue. We have delayed maturity so the juvenile stage is extended. As a result, the the adult is bigger.






We are dealing here with Peramorphosis, and more specifically Hypermorphosis. One or more populations of Estaingia has evolved, by Hypermorphosis into Xystridura. An event that occurred around the Lower-Middle Cambrian boundary, during a time of eustatic sea level fall that would have reduced shallow-water living space.

The take-home message isn't that trilobites are cool (they are), but that this brings out a very important point about evolution, and a good refutation of the old creationist canard, "if evolution is true where are the half-way transitionals? The half reptile-half bird?"

What these results show, is that evolution doesn't happen to all features at the same time, or at the same rate, producing a neat half-and-half transitional form. Some features change relatively rapidly (the expansion of the frontal glabella), some features change relatively slowly (head width to length ratio), and some don't change at all (the distance from the back of the eye to axial furrow distance as a ratio of head length). So there isn't a transitional which has all features exactly half way between the ancestral and descendant forms. What we find are transitionals with a mix of features depending on the rates at which those features are changing. We should not expect to find exact half-and-half transitionals. Evolution doesn't work that way.

de Beer called it "Mosaic Evolution". That isn't an excuse for the lack of half-and-half transitionals, it's a description of how evolution operates.


McNamara, K.J. (1981) Paedomorphism in Middle Cambrian xystridurine trilobites from northern Australia. Alcheringa, 5: 209-224. DOI: 10.1080/03115518108567002

Evolution Among the Trilobites Part 1

The last Palaeoporn featured the growth stages of meraspid, or juvenile, Estaingia. This post will use those meraspids and a bunch of holaspids, or adults, to measure the growth patterns of Estaingia, or it’s ontogeny.

Why? Because it’s important. It allows us to plot the growth patterns and if you know the growth patterns you can used them to look at evolutionary relationships.

If you want to look at evolutionary relationships between species there is one, and only one rule.

Ya gotta know what the kids are doing.
If you don’t know what the kids are doing, you can get, as some vertebrate palaeontologists are now finding, evolutionarily embarrassed. Ontogeny can provide clues to evolutionary relationships.

Studies of ontology requires the measurement of various features to show how they change with time or size (usually the two are interchangeable – in trilobites anyway). The changes in one feature are then compared with changes in another.

At right is the head of an average trilobite showing which bits are which. This post will be concerned only with the head and what happens to it during ontogeny. Actually its even more restricted than just the head. We'll only be looking at the cranidium. That's the central area including the bulbous glabella. Why? well we need to take a bunch of measurements over a range of specimens to build up a picture of the changes that occur during ontogeny. The trouble with the librigene or free cheeks is that they are, well . . . free, and tend to be lost (as pointed out in Palaeoporn 14 and 16). The cranidium is usually left behind and so is a better subject for measurements.

At right is a cranidium of an Estaingia. The relevant measurements that we are interested in are marked. CW is cranidial width, which is literally the distance between the eyes. PGF is Pre-Glabella Field which is the area in front of the large bulbous glabella. (Incidentally the pre-glabella field only runs to the shallow trench towards the front of the cranidium. In front of the trench is the doublure. That is folded underneath the cranidium in life, along the trench, and pops up during moulting (see Palaeoporn 16). GL is the glabella length. Adding PGF and GL gives us a value for the length of the craniduum. POG is Pre-Orbital Glabella which is the bit of the glabella that lies in front of a line drawn between the front tip of the eyes. AF-EL is the distance between the end of the Axial Furrow (the trench behind the glabella and the back tip of the Eye Lobe.

Lets show some measurements - the length of the central portion of the trilobite head, the cranidium, compared with the width of the cranidium, and the length of the glabella, for each specimen, as seen below
Here the measurements fall on a straight line. This is called isometric growth, where the ratio of the two features does not vary with growth. In example A, the ratio of the length of the cranidium to the width of the cranidium does not change with growth. In example B the ratio of the cradidial length to glabella length does not change. So during isotmetric growth there is no change in the shape. (What? Yes, OK, example A is not strictly isometric, since isometric growth always passes through the origin and a line drawn through the plot in A doesn’t. Just. But trust me, compared with what’s coming up next it’s pretty much isometric.)

Isometric growth can be very useful in confirming that specimens belong to a particular species. In the examples above, the red dots represent meraspid Estaingia and the blue dots holaspid, or adult forms. The fact that they all line up on a straight line is supporting evidence that the meraspids do belong to Estaingia. This is important because species are defined by a “type” specimen which is normally an adult, and so it can be quite difficult to place meraspids in the correct species if the growth patterns vary considerably from the adult.

Oh yes, the black dots at the far end of both graph trends represents a holaspid Estaingia from a different location and a slightly younger deposit, at Cymbric Vale in New South Wales (NSW Estaingia). Thought to be the same species as E. bilobata discussed here from the Emu Bay Shale, but also though not to be for a couple of reasons. It'll feature later but see how it plots along the same trend as the other specimens? good evidence that it is E. bilobata, but I'm getting ahead of myself.

Frankly, however, isometric growth while it has it’s place, is a bit boring. Meraspid 1 looks pretty much like the adult form. (no problem in putting the meraspids in the correct species there then.)

Just as well then that not all growth is isometric. In fact most growth patterns are not isometric, but anisometric. Anisometric growth, as you may suspect, is where the ratio does not remain constant, but changes during growth, and so shape changes during growth. Which means the meraspid can look distinctly different from the holaspid.

Holy rotating vectors Batman!
Now it gets interesting. There is only so much you can do with straight lines. Everything is better with curves! Anisometric growth changes are not random. They don’t occur because the merasid didn’t like the look of itself in the mirror. The represent hereditary traits. In the two graphs above, A shows Cranidial Width against Axial Furrow to posterior of Eye Lobe (as a percentage of cranidial lenght) (CW/AF-EL) and B shows Cranidial Length against Pre-Glabella Field (as a percentage of cranidial length) (PGF/GL+PGF).

Here the difference in growth patterns between the merasipd and holaspids is marked. This is telling us important information about how the final look of the holaspid form is achieved, and what pattern of growth occurred.

In graph A the feature being measured is the curvature of the eye. In early meraspids, the eye curvature is quite shallow and so the lower end of the eye is a significant distance from the Axial Furrow. As the meraspid grows, the eye curvature becomes more pronounced and the distance between the lower end of the eye and the axial furrow decreases. At the end of the meraspid stage, the distance (as a percentage of cranidial length) is around 0.25. In the holaspid stage this trend ceases, the eye reaches its maximum curvature, and doesn't change again, so the value remains at around 0.25. The NSW Estaingia plots along this holaspid trend albeit at a larger size that those at Emu Bay, but again, it is good evidence that NSW Estaingia is Estaingia bilobata.

In Graph B the preglabella field as a percentage of total cranidial length is plotted against cranidial length. Here the trends are different. In the meraspids, the preglabella field increases with growth until the Holaspid stage is reached. Then the trend is reversed and the preglabella field begins to reduce in size with growth, albeit at a slower rate than the meraspid rate. The NSW Estaingia again plot on the holaspid trend for Estaingia bilobata providing more evidence that the NSW Estaingia is E. bilobata.

One last graph which shows the preorbital glabella or POG (the portion of the glabella in front of the eyes).

Note that this is a mirror of the pregalbella field plot, and provides an explanation for the pregalbella field changes. The preorbital glabella in the meraspids decreases in size relative to cranidial length. In other words, as the cranidium increases in size, the preorbital glabella is increasing at a slower rate. This means that the area in front of it has to increase in size. So the increase in the pregalbella field we saw in the previous chart is a result of the preoccular glabella not keeping up during meraspid growth. However, in the holaspid stage, this trend is reversed and the preoccular glabella starts to grow at a more rapid pace than the cranidium generally, and begins to represent more and more of the total cranidial length. Thus the preglabella field begins to decrease as a proportion of the total cranidial length. Once again the NSW Estaingia plot among the Estaingia bilobata and along the trend. We can say with some confidence then that NSW Estaingia is a larger version of Estaingia bilobata.

Next time how these growth plots can provide information on evolutionary relationships.

Touring with Mr. Darwin

I've been meaning to blog this for a while, but have been too busy. I went to see the exhibition on Darwin at the National Museum of Australia, here in Canberra. It's good. It's very good!

The exhibits cover the world before Darwin, the young Darwin, the Beagle trip, the development of the theory, the theory and aftermath, and evolution today.

It's not large exhibition, but it does cram a fair amount in. The displays include writings, specimens, a mock up of Darwin's study, and AV displays - including three short films featuring evolutionary scientists such as Francisco Ayala, Francis Collins, Niles Eldredge, and Kenneth Miller. They also feature Genie Scott from the NCSE (join the NCSE today).

By far the most impressive pieces (and worth the price of admission on their own), are the writings of Darwin - notebook entries, manuscript pages and letters. Not copies, the real thing, pages, hand-written by Darwin himself. And not only from Darwin, there were letters from Hooker, FitzRoy, Wallace, and one from Huxley - that features the famous lines,

As for your doctrines I am prepared to go to the Stake if requisite... I trust you will not allow yourself to be in any way disgusted or annoyed by the considerable abuse & misrepresentation which unless I greatly mistake is in store for you... And as to the curs which will bark and yelp - you must recollect that some of your friends at any rate are endowed with an amount of combativeness which (though you have often & justly rebuked it) may stand you in good stead - I am sharpening up my claws and beak in readiness.

It's sad that, after 150 years, the curs still bark and yelp, but it's good to see that Darwin still has friends endowed with an amount of combativeness.

There were also family letters by Darwin, Emma Darwin, and Darwin's father.

The imagery and linkage they provoked was so palpable, it was almost like being in the room when they were written. I got positively goose-bumpy.

The highlight for me though, was the actual notebook, open to the page with the famous I think evolutionary tree (right). The actual notebook!

Wow! Like. Wow!

It's a good job it was in a plastic display case, because I think I was drooling à la Homer Simpson! To be so close to an image right out of the pages (literally) of science history!

The notebooks were amazingly small, no more that around 15 cms by 7 cms.

Interesting fact: Darwin wrote over 300 notebook pages on animals and plants, but over 1300 on geology.

One of the largest displays was a reconstruction of Darwin's study in Down House. This was very well done, and you almost expected Darwin to walk into the room at any moment! Quite poignant, was a shawl draped over the chair in the corner of the study. Late in life many images of Darwin have him wearing such a shawl.

This exhibit also had a brief description of Darwin's daily schedule, including his early morning walks around the Sandwalk - the walk behind Down House that Darwin used almost every day.

There was also a video of the Sandwalk, composed of still photos taken at 5 metre intervals all the way around the Sandwalk. So I took a stroll. I didn't see Larry Moran there though!

Interesting fact: only some 80 pages of the Origin manuscript survive. Darwin gave many of the manuscript pages to the children so that they could use the blank side to draw on!

The section on evolution today also carried the theme of controversy from when the Origin was released to the present. There was a short video describing the difference in use of the term 'theory' in science compared with everyday use. Genie Scott was front and centre again, along with a number of other scientists.

I noticed that, with the exception of Genie and Francisco Ayala (who could be dragged through a hedge backwards and still look elegant), there was a certain amount lacking in the dress sense department. Richard Fortey did look he'd just been pulled through a hedge backwards, and Niles Eldredge looked like he'd borrowed somebody else's suit! However, that really didn't matter, because science places more importance in substance than style, whereas ID creationism places style over substance - because they have no substance.

There was some coverage of ID creationism in the section on evolution today. It included an actual disclaimer from Cobb County Georgia,

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered.

I have to say it was much more disturbing in the flesh. Of course I've been aware of such disclaimers, and the litany of failures they have had in court, but to see one up close made it somehow more real, and not just something that was happening a long way away (even more reason to join the NCSE today).

All up, an excellent way to spend a couple of hours, and highly recommended.

Darwin is at the National Museum of Australia until the 29th of March.

Allopatric and synpatric speciation are the pits

Suvrat Kher in a comment to the ongoing discussion of pits here, asked:

"Are you applying this equally to both sympatric and allopatric modes of speciation? My thinking is that the difference between your speciation model and random drift model will be more apparent for the sympatric situation where natural selection may cause a divergence within a population while drift may not.

In case of allopatry both natural selection and/ or drift may cause divergence."

Yes, you are right. The first example shown would be allopatric sympatric speciation, as the new population forms from within the parent population.

Sympatric Allopatric speciation would be different, as it includes the physically separating of a sub-population from the parent population. In my model, this separation would also occur in morphospace instantly, as the allele frequency of the parent population has changed.

While the allele frequency of a population is an average over the whole population, this frequency would not occur at every point within the population. At any given point some allele would be more frequent, others less frequent.

If a sub-population becomes isolated, it's allele frequency will not change much, but the allele frequency of the parent population will. This is because some allele have now been relatively concentrated in the parent population (those alleles occurring less in the sub population), compared with others that have been relatively diluted in the parent population (those occurring more in the sub-population).

Thus, in this model, isolation would be represented as a shift in the position of the parent population in morphospace, with the sub-population orbiting close by.

I'll try and get some diagrams up shortly.

New Scientist - Again

The latest round in the New Scientist cover 'story' is the editorial by New Scientist. PZ Myers thinks it goes some way to defuse the situation, which surprises me, because I don't think it does.

Here's the disclaimer editorial in full (it can be found here)

"THERE is nothing new to be discovered in physics." So said Lord Kelvin in 1900, shortly before the intellectual firestorm ignited by relativity and quantum mechanics proved him comprehensively wrong.

If anyone now thinks that biology is sorted, they are going to be proved wrong too. The more that genomics, bioinformatics and many other newer disciplines reveal about life, the more obvious it becomes that our present understanding is not up to the job. We now gaze on a biological world of mind-boggling complexity that exposes the shortcomings of familiar, tidy concepts such as species, gene and organism.

A particularly pertinent example is provided in this week's cover story - the uprooting of the tree of life which Darwin used as an organising principle and which has been a central tenet of biology ever since (see "Axing Darwin's tree"). Most biologists now accept that the tree is not a fact of nature - it is something we impose on nature in an attempt to make the task of understanding it more tractable. Other important bits of biology - notably development, ageing and sex - are similarly turning out to be much more involved than we ever imagined. As evolutionary biologist Michael Rose at the University of California, Irvine, told us: "The complexity of biology is comparable to quantum mechanics."

Biology has been here before. Although Darwin himself, with the help of Alfred Russel Wallace, triggered a revolution in the mid-1800s, there was a second revolution in the 1930s and 1940s when Ronald Fisher, J. B. S. Haldane, Sewall Wright and others incorporated Mendelian genetics and placed evolution on a firm mathematical foundation.

As we celebrate the 200th anniversary of Darwin's birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that "New Scientist has announced Darwin was wrong". Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not.

Nor will the new work do anything to diminish the standing of Darwin himself. When it came to gravitation and the laws of motion, Isaac Newton didn't see the whole picture either, but he remains one of science's giants. In the same way, Darwin's ideas will prove influential for decades to come.

So here's to the impending revolution in biology. Come Darwin's 300th anniversary there will be even more to celebrate."

This indicates that New Scientist knew exactly what damage the cover could do, but instead of stopping the damage, went after the money, and used the editorial to cover their backsides when the inevitable excrement hit the spinning blades.

This editorial is simply New Scientist saying, "Don't call us a goose just because we laid a golden egg for creationists. Look at the pretty words."

But it even fails that, for two reasons.

1) Creationists are not going to read the editorial. The people in the audience when the cover is shown, will not read the editorial. The school boards to whom the cover will be shown as evidence that evolution is wrong, will not read the editorial.

PZ thinks that this paragraph may work:

"As we celebrate the 200th anniversary of Darwin's birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that "New Scientist has announced Darwin was wrong". Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not."

Somehow I don't think a creationist presenter will wait politely while someone interrupts the presentation to read out these 72 words. 72 words. Against 1 picture.

If a picture is worth a thousand words, 72 doesn't quite seen enough, does it.

2) The editorial hands some more golden eggs to IDiots!

Lets see how an IDiot would read this:

"If anyone now thinks that biology is sorted, they are going to be proved wrong too. The more that genomics, bioinformatics and many other newer disciplines reveal about life, the more obvious it becomes that our present understanding is not up to the job. We now gaze on a biological world of mind-boggling complexity that exposes the shortcomings of familiar, tidy concepts such as species, gene and organism."

A particularly pertinent example is provided in this week's cover story - the uprooting of the tree of life which Darwin used as an organising principle and which has been a central tenet of biology ever since (see "Axing Darwin's tree"). Most biologists now accept that the tree is not a fact of nature - it is something we impose on nature in an attempt to make the task of understanding it more tractable. Other important bits of biology - notably development, ageing and sex - are similarly turning out to be much more involved than we ever imagined. As evolutionary biologist Michael Rose at the University of California, Irvine, told us: "The complexity of biology is comparable to quantum mechanics."

"See", they'll say,"New Scientist agrees that life is too complex for Darwinism to explain. It must have been designed."

New Scientist, you're a goose!

New pits - now with diagrams!

I've been discussing pits here, here, and here, if you are interested, but so far without diagrams. There's a reason for that. I'm rubbish at diagrams. OK, I don’t have a decent graphics program, but that wouldn’t matter anyway. I'm still rubbish. That’s why I prefer my fossils in 2D! However, here is an attempt at a graphic representation of what I’m talking about.

The first diagram represents speciation via a concentration of alleles, adaptation, whatever.

A) This represents the current species as a morphospace topography. The shape doesn’t really matter, nor does the orientation, as in morphospace all three dimensions are equal, and there is no “up” or “down”. The shape is just to invoke some idea of 3D. If you want to get fancy, there may be gaps on close-up, but for now we are just giving an impression of the extent of the topography that defines this species. Basically the topography represents the extent of allele distribution that represents this species.

B) A beneficial allele appears at a location and its presence in the populations begins to increase preferentially. The circle represents the increasing occurrence of the allele.

C) Frame of view rotated to show what’s happening underneath. The allele increases in concentration at this location faster than it occurs elsewhere in the population, and so the topography warps in response, forming a pit. As the allele concentration increases, the local allele distribution departs from that of the surrounding ‘normal’ allele population and so the bottom of the pit continues to move away from the ‘normal’ topography. (This is pretty much the same as the Mt. Improbable version, but reversed.)

D) Speciation! Well incipient speciation anyway. The local allele distribution departs from the ‘normal' to the extent that further interaction with the original species ceases. The new population is now isolated and begins to change independently of the original species.

E) Speciation. The new daughter species is established. The new species clusters together with the old species in morphospace, since they share far more alleles that the new species shares with any other species out there. The topography of the new species is similar to the old species, which also to invokes a relationship. There is no connection between them, so no allele swapping, so a new species. The topography of the old species also changes slightly due to the change in allele frequency.

OK now lets see what happens what the daughter species starts the same speciation process.

A) A beneficial allele occurs and starts to become preferentially concentrated at one location in the population. The pit forms and continues to grow as the concentration of the beneficial allele continues to increase. This time the pit isn’t ‘downward’ because there is no ‘down’. The pit forms at 90 degrees to whatever the surface orientation is.

B) Incipient speciation as before, with the new population separated from the main population.

C) The new species is established, and again clusters close to the parent species as they share more alleles in common with each other than they share with any other species.

This group could also be classed as a Genus as we have a direct ancestor-descendant relationship. Also we can wind the tape back and show that relationship as the daughter species run back into original species.

This model is also internally consistent, because the topography can represent the origin of species, genera, families, even phyla. The same process, the same imagery. It's like a Mandelbrot set, with the same imagery showing species, families, or phyla, depending on the magnification.

For example, the first diagram could be used to represent the evolution of birds from dinosaurs (albeit very crudely - it'll need some work), with the original topography representing dinosaurs and the daughter "species" representing birds. In this instance, the next image in the sequence "F" would show the dinosaur topography shrinking, and eventually disappearing altogether as the as the dinosaurs moved towards, and finally became, extinct.

As a bonus, here's how genetic drift would look like.

A) The morphospace topography of the population.

B) A new allele occurs and starts to spread in the population.

C) Instead of being preferentially concentrated in one area as a beneficial allele would, the allele slowly increases by spreading out into the surrounding population. In other words it spreads out 'faster' than it concentrates in one location.

D) The new allele is fixed in the population, causing the topography to change somewhat as the new allele frequency is slightly different than the original one.

Johnny, I'll try and get around to your questions in the next couple of days.

Even more pits

OK this is the latest in an ongoing conversation I'm having with Johnny on the issue of pits, the first two installments can be found on his blog Johnny provided some comments on my previous pit post and I have brought them up to the front to answer them. Johnny's comments are blockquoted.

Since we agree that Mt. Improbable is a good analogy for its intended purpose, I’ll move on.

Um, hang on. I say that Mt Improbable is ok as far as it goes. The problem is that it doesn’t go very far! The analogy doesn’t cover all evolutionary processes, only adaptation. There is no climbing involved, and evolution is directionless, it doesn’t proceed upwards. So, apart from that, yeah, it’s OK.

Viewing the two blog post here, as well as the two comments you were kind enough to provide to the “rebuttals” at my site, I think that, broadly speaking, there are a couple of assumptions or implications being made that are fundamentally false – false, based on my understanding.

1. You describe Natural Selection as acquiring beneficial alleles through a “random process.” This is incorrect; NS is a non-random cumulative process.

The generation of alleles is random, the concentration of them may or may not be. The concentration of beneficial alleles is non random, but “non-beneficial” alleles can also be fixed.

2. You imply that genetic drift contributes to fitness when, in fact, drift is a random process that is entirely disconnected from fitness. (Big point)

Actually I didn’t mean to imply that GD contributes to fitness. It may do, if the fixed alleles subsequently provide the starting materials for beneficial alleles, but at the time, no, there is no increase in fitness.

3. Through descriptions of lateral jumps between peaks, distances between pits and by suggesting that new “groups” can arise by “breaking through new fitness landscapes,” you’re implying that a Genus, Class or Family can erupt from a Species. This is false. Species rise from “speciation” at the species level. There is no jumping between points – only steps - a continuous gradation.

I’m a bit confused here. Genera, Classes and Families, while artificial constructs, are formed initially from one species – the common ancestor of the group. The original population undergoes a concentration of alleles into a pit which sags If that concentration of alleles becomes intense enough, ‘bottom’ of the pit separates from the original population’s topography, producing a new species (if there is no link then there can be no allele transfer = genetic isolation and so a new species.) We now have two species, represented by the original topography, and the new topography, species 2, which is orbiting close by. Say the original species undergoes another speciation event to produce species 3. Now we have three species cluster closely together in morphospace, as they share more alleles in common with each other than they do with any other species.

This grouping of the common ancestral species and its descendant species would comprise a genus, but with the caveat that the boundaries of which species would be classed as in the genus or outside is an arbitrary one. Speciation still occurs over time, with no major jumps.

4. You imply that “Generalist” and “Specialist” are definitive forms by saying that one has survival value over the other. These are relative terms. You may view/classify a particular insectivorous mammal as a specialist because its diet is limited to only insects – I could counter by saying that it’s a generalist because it eats a wide variety of insects as oppose to limiting its consumption to termites. Without knowing the type and extent of a theoretical catastrophe – there is absolutely no way to predict what niches will remain intact or the rate to which any event survivors will rebound.

There is no doubt that specialists can be very successful, and you are right that there is no telling which niches will survive. But specialists with adaptations to a specific environment may well be at a disadvantage should the environment shift and close out the niches to which it has become adapted. Under those circumstances the species is carrying a load of alleles that are no longer useful. If those alleles produce adaptations that have a high production and maintenance cost, then they are disadvantaged compared with other species which, while not dominant in the previous environment, do not carry the extra load and so may be in a better position to survive.

On an individual species basis significant adaptation may well provide dominance in a certain niche, but that species is more likely to disappear if the environment changes compared with other species that are more general and hence can survive in a number of environments. Generalists generally do not dominate any niche, but exist in several. Specialists dominate in one niche.

5. You create a false dichotomy between peaks and pits; both are landscapes and as the term “landscape” suggests, both represent a varied ever changing state complete with valleys, ridges, prairies, bumps, holes – they are one in the same –metaphors for change.

Yes, but as I mentioned above the Mt Improbable analogy doesn’t cover all evolutionary processes, only adaptation. There is no climbing involved, and evolution is directionless, it doesn’t proceed upwards.

6. You imply that organisms adapt or imbed themselves into a static environment, when in fact static environments don’t exist. Ecology is a balancing act, therefore so is adaptation.

The environment is not static, and adaptation works to balance this, but become too specialised, and have the environment shift too much, and the species is left high and dry.

7. When comparing short-term success with long-term survival you seem to suggest that evolution is a fundamentally different process following some catastrophe or major ecological shift. This isn’t so; the same processes driving speciation, drift and natural selection today are the very same processes that will drive evolution following an asteroid impact. If adaptation and specialization are what is successful in the here-and-now, they are also going to be successful strategies following a catastrophe.

Actually, evolutionary processes are the same, it’s just that after a major ecological shift it is more like to be generalists that repopulate first and become the source of new species (yes, by adaptation).

8. Describing both Natural Selection and Drift in terms of allele frequency is fine; however keep in mind that NS works with phenotypes as well as genotypes; this builds the link to fitness. Drift does not have this link.

Yes Natural Selection works well, there’s no argument there. But NS isn’t the only process at work, and the Mt Improbable analogy only covers adaptation. A description that covers all evolutionary processes would be better.

9. The idea that a current level of adaptation exhibited by an organism somehow reflects its future potential or its available genetic plasticity is erroneous.

OK, what if we have two organisms. A with small feet adapted to dry ground and B with larger feet. A is dominant in the environment, but B is OK on dry ground, but can also access marshy ground. Now, suppose the environment changes to all marshy ground. Can we say nothing about the future potential of these two organisms?

However, I do admit, the visual image of a “sag” being created by the weight of an area with increased allele concentration is pretty catchy…

Yeah, one does tend to gravitate towards it . . .

More Improbable Pits

The reasoning behind all this is not to attack the Mt Improbable analogy – which is to show that you do not need large-scale jumps to produce adapted forms, but that they are produced through gradualistic processes.

And a good job it does. What I am looking at here, is whether we can formulate an analogy that can be expanded to encompass more of the evolution process, and hence a series of internally consistent descriptions. The Mt Improbable analogy was not formulated to encompass the depth and range of evolutionary processes, and it would be wrong to criticise it on that score.

Close scrutiny of the Mt. Improbable analogy shows that there may be better ways to represent adaptation that can be expanded to other representations of evolution in a consistent way.

Riding Mt Improbable
Adaptive or fitness peaks are a reflection of the current state of allele frequencies. In other words they reflect which allele frequencies are delivering advantages in a particular environment (advantage = greater reproductive success = a higher concentration of alleles). They do not represent the best possible frequency/fitness solution to a particular environment – such a solution would be impossible, or at least constantly changing - influenced as it would be by the environment, the starting point of allele frequencies, and new alleles produced by mutation (and also impossible to achieve as adaptive success would be 'better than everyone else', not the best possible - which is similar to the old joke of two hikers being chased by a bear. Hiker 1 stops to put on a pair of running shoes. Hiker 2 says, "They wont help you outrun the bear”. Hiker 1 says, "I don't need to, all I need to do is outrun you".)

Peaks represent actual frequency/fitness values measured from actual populations/species. Since this is the case, a population/species sits on top of a peak, because the peak is defined by it. In other words the peak represents a particular groups of alleles that produce an advantage and hence are reproductively favoured, and so are concentrated at that point. The greater the concentration here, as opposed to elsewhere in the population, the greater the peak.

Therefore a population always rests on the peak. As the alleles continue to provide an advantage, the concentration of those alleles increases and the peak increases in ‘height’ (or more accurately distance from the fitness plain). Imagine a lava lamp. Once warmed up, a central peak starts to form. As the heat increases, the peak ‘grows’ upward. This is what is happening in the fitness landscape. The population/species sits on the peak and the peak grows underneath it upwards away from the landscape, as the allele concentration increases.

This means that there is no climbing involved. We should be taking about Riding Mt Improbable, not climbing it!

More than adaptation
The next issue we have is how to describe speciation. With the Mt. Improbable analogy this would result in peaks sprouting from peaks like horns, as populations split. The analogy therefore starts to groan under the strain of trying to be consistent. Again I wish to emphasis that the analogy was not meant to do this, and so this is not a criticism, I am pointing out that maybe there is a more consistent analogy we can use.

The other problem is that the peaks are still attached to the fitness landscape, which implies that there is still a route that populations can take to follow in the footsteps (slime trail?) of the new species. In truth, this would not occur, as once the new species has been formed, all connection with the ancestral population are severed. So we would end up with isolated ‘peaks’ suspended above fitness plains, again stretching the Mt. Improbable analogy too far.

"My God, it's full of pits"
So can we establish an analogy that can be expanded to fit into a more encompassing explanation for evolution generally? I think we can.

Firstly we need to explain the fitness landscape. A possible better analogy is one where populations occupy discrete areas, or topographies, of morphospace. Morphospace itself can be considered as an essentially limitless three-dimensional space within which morphospace topographies describe populations.

These topographies can be any shape as there is no “up” or “down”. Populations are described by the current spread of alleles, and so only areas that correspond to current allele frequencies have a topography. No populations, no topography, just empty space. Populations can expand into empty space as allele frequencies shift, or contract to leaving empty space – if they contract far enough, they disappear = extinction. But there is no set landscape that populations occur in. Populations define the extent of the topography.

OK, a population defines a topography that can be any shape. As the alleles in the population shift, the topography shifts. In this analogy, alleles that confer an advantage become concentrated within a sector of the population. This causes the topography to sag. As the advantage continues and resulted in reproductive success, the allele concentration increases, increasing the depth of the pit gradually (though not necessarily constantly). It should be noted that, since the topography could be any shape and orientation, the direction of the pit could be horizontal, vertical or anything in between, as the sagging will be at 90 degrees from the surface topography (which could be at any angle). This does away with the implication (unintended as it is) from other analogies that evolution is directional and upwards.

The pit therefore describes the state of the population in terms of allele frequency, with the bottom of the pit representing the highest concentration of the advantageous alleles and the sides representing decreasing concentrations of the allele. So if people ask how did the population get to be in a pit so deep in one go, to answer, hand them a shovel.

Speciation occurs when the pit separates from the rest of the topography. This does two things. It forms a satellite topography that represents an independent population – a new species – which is free to form it’s own topography, and start the formation of new allele concentrations and eventually new species.

It also causes the topography of the old population to retract away from the new topography as the allele frequencies realign back towards the old population frequency since there has been a significant removal of alleles with the new species.

A word here on genetic drift. The Mt Improbable analogy doesn't cover drift. But in my anaolgy, drift would be represented by a broad shallow pit as the allele becomes incorporated into the population faster that it is at the point of initiation so the pit expands outward through the topography rather than into a pit. Drift is then a ripple in the topography that, once fixed, leaves the topography slightly lower/higher that it was prior to the fixation event.

Separate topographies = no allele transfer = species. It is possible that the old population has retained enough of the advantageous alleles that the separate populations grow back together. But that would need to happen very quickly, before the frequencies become to divergent (as in populations that are geographically isolated but can still share alleles if brought together).

So a cluster of interconnected topographies, and some closely aligned but separate topographies, denote a species. This is the highest magnification. Ratchet the magnification back a notch, and clusters of closely positioned topographies become Genera. Ratchet back again and clusters of genera topographies become Families, etc. The closeness of topographies between separate species, genera , etc can make the decision as to which topographies go where, difficult - as in real life.

Ratchet the magnification back far enough and we can see the all of current life on Earth represented.

But, it would show relationships as they are today, with groups occupying discrete areas of morphospace, separated from each other. It cannot show the connectedness of life because we are viewing it as it is today, after 3.5 billion years of evolution. To show the connections, the evolutionary relationships, we need the 4th dimension – time.

What we can do is run a time sequence backwards, that would show morphological topographies coalescing, firstly species recombining backwards into founder species, then genera, etc, until we see the major groups contracting back together, metazoan topographies coalescing back into single celled topographies, eukaryote topographies coalescing back into prokaryote topographies etc.

Running the sequence forwards we would see the reverse. For example, it could show the origin of the dinosaur topographies from other reptile topographies. Such topographies would increase in number and morphospace coverage, and then start to shrink back over time, but one group of topographies produces a flurry of new topographies that expands and continues to develop and produce new offshoots, even as the main dinosaur topographies reduce in number and finally disappear. This new group of topographies would be the birds.

The pit analogy would then, connect with a more internally consistent consistent group of analogenic (is there such a word?) descriptions of evolution.

It’s pit’s all the way down!

Told ya so!

And for my next trick, this weeks lottery numbers will be . . . .

Last year (well all right, December 31 2008), I blogged about how certain phrases in science papers could have been better constructed to avoid misrepresentation and quote mining by creationists.

The example I used was:

The size increases appear to have occurred when ambient oxygen concentrations reached sufficient concentrations for clades to realize pre-existing evolutionary potential, highlighting the long-term dependence of macroevolutionary patterns on both biological potential and environmental opportunity. (emphasis added)

From Payne, J. L. et al. (2009) Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Proceedings of the National Academy of Sciences, 106(1): 24-27.

Today, PZ Myers had blogged that the creationists are using this exact quote to support their discredited views.

Told ya! And yes, I'm looking at you Eamon Knight! :-)

Climbing Pit Improbable

In the ongoing Adaptationist v. Pluralist debate, both sides agree on a surprising amount. Both sides agree that there is more to evolution than adaptation by natural selection. However, Adaptationist would argue that adaptation by natural selection is the most important, or even the overwhelming, evolutionary process, and that evolution can be described as climbing Mt. Improbable – with adaptation to environment similar to climbing a fitness landscape peak towards optimal fitness (but please note, never, ever, reaching the top!)

I disagree. I think genetic drift accounts for most of the evolution that occurs, and natural selection, while very important – especially in creating diversity – accounts for a smaller percentage. However, both have worked together to produce the diversity of life on Earth.

I also have a problem with the Mt Improbable analogy . . . well, actually I have two problems.

1) It perpetuates the idea that evolution is an upward striving process, and that derived or adapted groups are higher, than the less derived or less adapted and, as a consequence, fitter, advanced . . .better. (the old Tree of Life analogy problem.)

OK, maybe it is applicable to a fitness landscape, but there is no reason that the landscape has to have the peaks pointing upwards, . . . is there? Surely it's the distance between where you are on the peak and the schmucks on the fitness plane that is important, not the direction of that distance?

Plus, fitness landscapes, are not permanent, or even solid. They change with the environment. A population/species, or whatever, may be quite "high" (see how hard it is to use neutral language)on a fitness peak one minute, and find itself down on the plane, or even in a fitness trough, with hardly any change in allele frequency, but a significant change in environment. In other words the fitness landscape moved underneath it.

2) The real problem with the Mt Improbable analogy though, is that it gives the impression that as hard as it is to ‘climb up’ (and it is), the analogy suggests that it is relatively easier to ‘climb down’ - and it isn’t because its actually harder. OK that might be pushing the analogy a bit far – but that’s the point, it doesn’t hold up to detailed scrutiny.

The real problem is that adaptation, in the broader picture, is an evolutionary cul-de-sac.

Adaptation means that certain alleles are being selected for because they confer an advantage in a particular environment. If the environment changes, then the alleles that conferred an advantage may no longer do so. Worse, the very process of selecting for certain alleles may well have stopped other alleles getting fixed through drift – alleles which might be beneficial in the new environment. Even worse, the alleles that were originally selected for may be costly to produce and maintain where they confer no advantage, and thus be deleterious.

But the really bad thing is that, as hard as it is to gain the alleles that provided an advantage, it is even harder to loose them, as this would require specific mutations to affect those particular alleles (rather than the random process that produced them). You could reduce them to a vestigial level, provided you survived long enough to do so. Difficult though, if you are struggling to survive in a new environment where the competition does not have the adaptive dead weight (unless you have some other advantage.)

The more adapted a group becomes, the more imbedded it is in a particular environment, and the more sensitive it is to changes to that environment.

Eventually all strategies lead to extinction, but during environmental change, it’s the generalists that survive, not the specialists. Adaptation generally leads to extinction. Highly adapted groups/species and ecosystems delicately balanced on a web of interconnected adaptations, will crash once environments change.

Adaptation is not climbing up Mt Improbable, it’s climbing down Pit Improbable! The pits are hard to find, but once in, it’s easier to go down than it is to back out, and if you adapt too far, you are trapped in a cul-de-sac with no way out when the environment changes. The generalists that flirt with the rim of the pit, or on the fitness plane have a better chance of surviving to become the stem stock for new adaptations.

It may well be that some species or groups of species in a pit break through to new fitness landscapes and produce new groups (e.g. birds and mammals from reptiles) because fitness landscapes are not flat, but curved.

But for most populations/species, adaptation is a pit of no return.

Photo credits
Mountain image from copyright-free-photos.org.uk
Pit image from larrydsmith.com


UPDATE
There are two discussions here and here, and a new blog post here.

Pedantic pedantry 1

OK, This is going to be an occasional series where I highlight where certain phrases or statements in the current science literature could have been . . . um . . . better thought through? Yes, better though through. Because as written, provides inadvertent fodder for the creationists/IDiots to quote mine.

Having some considerable experience with the various forms of creationism from Young Earth to ID, a common thread through most creationist claims is the misrepresentation of the scientific literature by taking short piece out of context or a single phrase or sentence to support their claims, when the piece as a whole clearly doesn’t. The creationist quote mine has been documented many times, and to be fair to creationists, is also employed by both AIDS deniers, and climate change deniers.

In order to starve the quote miners, authors need to be very careful in their phraseology. And so here is my contribution (every little helps, but this is also a case of those who can, write, those who can’t, contribute)

PP1 comes from:
Payne, J. L. et al. (2009) Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Proceedings of the National Academy of Sciences, 106(1): 24-27.

The paper discusses an increase in body volume of 16 orders of magnitude for living organisms over the last 3.5 billion years, with two pronounced jumps of approx. 6 orders of magnitude 1.9 billion years ago and between 600-450 million years ago hence my interest). It is claimed that these two jumps are related to increases in the ambient oxygen concentration.

The statement under consideration here is the concluding sentence of the conclusion:

The size increases appear to have occurred when ambient oxygen concentrations reached sufficient concentrations for clades to realize pre-existing evolutionary potential, highlighting the long-term dependence of macroevolutionary patterns on both biological potential and environmental opportunity.

*polite cough* (See – I’m being polite)

The problem here is the phrase pre-existing evolutionary potential.

I’m going to assume here that the authors (all 13 of ‘em) didn’t mean to imply that evolution pump-primed organisms with abilities and then waited around until the conditions in which those abilities would be useful, occurred. In other words, the ability of organisms to grow big occurred in anticipation of the right environments that would allow such growth – which is what creationists will claim it says. See they will say, scientists say organisms were provided with pre-existing abilities prior to those abilities being useful. Only God a Designer could do that.

Undoubtedly what the authors intended was to say, was that, as increasing oxygen levels expanded the area of morphospace available for evolution to operate in, some clades that acquiring separate features to scavenge oxygen from the environment (gills), and a mechanism to transport that oxygen deep into the tissues (circulatory system with some oxygen-hugging components)- which was very useful even at lower oxygen concentrations - evolve larger forms as the ambient oxygen concentration increased. And not, that the features previously mentioned evolved to take advantage of future increases in oxygen levels.

Please remember – as far as creationist quote miners are concerned, it’s the words that count, not the intent.

Steven Jay Gould

I'm a big fan of Steve Gould. I don't agree with all of Gould's views, but I find I am in much more agreement with them than the 'British School', or adaptionists - which I find to be somewhat stagnant of late.

Anyhow, there are a couple of recent blog posts about Gould that I think deserve greater circulation, so they are here:

Sandwalk - An Adaptionist View of Steven Jay Gould

Laelaps - Stephen Jay Gould's view of life

Enjoy.

Will the real Cambrian Explosion please stand up

OK, now I’m really pissed! No, it’s got nothing to do with the bottle of fine South Australian Red I’m soothing my pent up frustration with. It’s another bloody antievolution ‘expert’ mangling the Cambrian Explosion. Again!

Look. People. Let’s be clear about this. Please be specific when you are talking about the Cambrian Explosion. At least identify WHICH Cambrian Explosion you are talking about.

Cambrian Explosion One is the evolution and consolidation of a number of new body plans (disparity) which occurred over an extended period of time, and started well inside the Ediacaran. This was a true exploration of morphospace - groups boldly going where no group had gone before. Really.

Cambrian Explosion Two is the rapid expansion of the Cambrian fossil record. Which, while an evolutionary event, was primarily a biochemical event – namely the rapid take up of the idea that playing around with carbonate or phosphate mineralisation was right up the in the list of brilliant tactical maneuvers. Be it for digging burrows, chewing on everyone else, or stopping everyone else chewing on you. It was a diversification event – by comparison, exploring the local region of morphospace (boldly going where no group had gone before but within reasonable parameters, and we promise we’ll be back for dinner.)

Cambrian Explosion Two is to evolution what the microwave background radiation is to the Big Bang (kind of).

It’s the bit we get to play with after the major event.

So, the next time some antievolution 'expert' prattles on about the suddenness of Cambrian Explosion Two (and so Cambrian Explosion One was sudden), ask 'em WHICH Explosion they are on about, and do they now the difference between boldly going where no group has gone before, and swanning around the solar system?

Oh, and it’s a Wynns Coonawarra Cabernet Shiraz Merlot 2001. Thanks for asking.

The Spandrels of San Marco and the Anomalocaris Paradigm

The Spandrels of San Marco and the Panglossian Paradigm is one of my favourite science papers. As someone who accepts natural selection as a powerful evolutionary mechanism, but who considers that there are other, equally, or perhaps more, powerful mechanism out there, such as genetic drift, this paper resonated a lot with me. To summarise the paper (if you haven’t read it, please do), not everything that happens in evolution occurs because it was selected for. Like spandrels, things can happen as a consequence of other events. To summarise the summary, sh*t happens.

Here I’d like to develop that theme using Anomalocarus.

Anomalocaris was a torpedo-shaped, 1+ metre, top-line predator in the Early Cambrian oceans. It had a nasty set of jaws set in a circular mouth and a pair of muscular spiny appendages
hanging praying mantis-like from the head, and a pair of large bulbous eyes. It was a mean bugger. If the kids that burn the wings off insects had aquaria, this is what they’d want in it. We’re talking the king of the Cambrian. Nasty.

Big predators need big prey and Anomalocaris ate trilobites, big trilobites, big spiny trilobites. In this case, Redlichia. (see image. Scale bar at top = 1cm)

Think of Redlichia as having the style, sophistication, and armour plating, of an Abrams tank. Not the quickest trilobite around, not the most manoeuvrable, but not so much of a problem when, you’re up to 20 centimetres long, and the only thing that big enough to eat you is Anomalocaris, especially when the jaw elements of Anomalocaris were less strongly mineralised than Redlichia, AND, the jaw elements couldn’t actually bite together!

Hang on. If the jaws were less strongly mineralised, and didn’t even come together strongly, just how could Anomalocaris eat Redlichia?

Well we have evidence that Anomalocaris did indeed eat Redlichia – trilobite fossils with great wedge-shaped bite marks that had to have been made by Anomalocaris, and fossil poo of broken Redlichia fragments of a size that could only have been delivered by Anomalocaris (at least we haven’t found anything smaller with an appropriately pained expression). Anomalocaris was able to dine on Redlichia by exploiting a weakness in one of the most successful body parts ever to have evolved, the arthropod exoskeleton.

OK, a quick intro to arthropod exoskeleton

Arthropod exoskeleton gets its mechanical properties primarily from a bilayered construction, consisting primarily of a thin, usually mineralised, outer exocuticle, underlain by a thicker, unmineralised, endocuticle. Each of these brings a differing mechanical property to the exoskeleton. The hardened exocuticle is strong (and thus resistive to cracking) under compression (or being poked), but weak (and vulnerable to cracking) under tensional forces (or being stretched). By comparison, the softer, more pliant endocuticle is the opposite, weak under compression, but strong under tension. These properties combine to provide a greater level of protection against mechanical attack than either layer could alone, especially against normal predation, which pushes down, producing compressional stress on the exocutile, and causing the underlying endocuticle to stretch around the pressure, producing tensional stress on the endocuticle.

By varying the thickness and mineralization of the two layers, arthropods can produce a wide range of exoskeleton types, from stretchy elastic to hard rigid.

(There’s a lot more to arthropod cuticle, but that’s enough to be going on with.)

Ok, so how does this help Anomalocaris, and where is the weakness? Well, what Anomalocaris did was to attack from the side, reach over the top of the trilobite with its two appendages and grip the far edge of the trilobite, wedging it between the spines on the appendages. It then pushed the near side of the trilobite into its mouth and pinned the trilobite in its jaws somewhere between the near side and the middle of the body. Now comes the neat bit. Anomalocaris would then pull up with its frontal appendages (no doubt assisted by the large muscles in the head) and flex the trilobite - almost like trying to roll the far side of the trilobite around to the near side to make a tube. Then Anomalocaris would reverse the process. Flexing one way imparts compression stress on the exocuticle and tensional stress on the endocuticle and flexing the other way reverses the stresses so that the exocuticle is under tensional pressure and the endocuticle is under compression. And as strong as both are in one stress field, they are weak in the other field. Flexing back and forth quickly induces fractures in the cuticle, which propagate and finally result in failure, allowing the Anomalocaris to break off large chunks of juicy trilobite.

You can mimic this process using a credit card (preferably an expired one). It’s impossible to break a credit card by poking at it with your fingers. But, if you grip it in both hands by the short edges and flex it back and forth, a line of weakness quickly forms, as plastic is weak in tension and the stretching motion quickly weakens the card. Pretty soon you can break the card as a crack propagates along the line of folding. Substitute appendages and mouth for your right and left hands and this is essentially what Anomalocaris does.

All well and good, but what has all this to do with evolution and spandrels?

Well, the thing about trilobites is that, as arthropods, especially arthropods with armour plating, the only way they can grow is by moulting.

Just as crabs do today, trilobites had to escape from the exoskeleton they were living in order to grow. They would emerge soft and squidgy, pump themselves up to the new size and then harden the new exoskeleton.

Prior to moulting, arthropods made changes to the cuticle that made it brittle and easy to crack. To further help the moulting process in trilobites, there were a series on lines of weakness, called suture lines. These were the first things to break once moulting started, and so aided the process. They can be seen in the Estangia photo at the top left of this blog. The crescent-shaped structures on the head, either side of the central bulbous glabella, are the eyes. The line running behind the eye and continuing on to the back of the head, is a facial suture. It continues from the top of the eye to the outer margin of the head – best seen on the left side of Estangia, where the whole area of the head outside of the suture line has been displaced (called the ‘free cheek’ for this reason). This shows that the specimen is a moult. Once the suture lines had parted, the trilobite would exit the old exoskeleton through the head region.

The reasons for suture lines around the eyes are obvious. It was important to ensure that the eyes were easily released during moulting, as the trilobite was vulnerable, and needed the eyes free to keep watch.

However, moulting is a hit and miss affair. Problems can occur. For example the facial sutures may not break easily. Trilobites having difficulty moulting would be in trouble, after all, it’s not like they could ask for help! A trilobite thrashing around on the sea bed trying to moult would draw attention to itself at a very vunerable time.

The problem for big Early Cambrian trilobites like Redlichia is that they had limited flexibility (curling head to toe). This meant limited options should anything go wrong with the moulting process. And things went wrong - I collected a Redlichia specimen where the left free cheek was upside down, the right was implanted into the sediment at 90 degrees, and the body has split into three parts. It had either undergone a horrendous moult, or had just had the best sex of its life!

So anything that assisted the moulding process would be advantageous

The ability to enrol the body (curling the body so that the head tries and meet the tail, with the legs tucked in between), even part way, would clearly aid moulting as it would stretch, and put pressure on, the exoskeleton and suture lines. So its of no surprise that by the end of the Cambrian all trilobites could flex to a fair degree, and some could almost touch head to tail. Estangia was well on the way to being able to do it in the Early Cambrian.

Enrolling has such an obvious benefit to trilobites generally that it isn’t surprising that it is a common, in fact pretty much ubiquitous, feature of trilobite after the Cambrian (the group that Redlichia belonged to never made it out of the Cambrian). Even the itty-bitty trilobites that Anomalocaris wouldn’t be seen dead eating (or rather would be seen dead as small trilobites wouldn’t provide enough energy to warrant the chase. Imagine a whale eating krill, one at a time!) It’s clear then that enrollment was probably selected for as an aid to moulting as pretty much all trilobites after the Cambrian could do it to a significant degree.

But, and here’s the kicker (finally), enrollment – even partial enrollment achieved by some Cambrian trilobites – negates the Anomalocarus predation method.

A curved trilobite cannot be flexed back and forth like a relatively flat trilobite can. To go back to the credit card analogy, imagine trying to flex a curved credit card.

Clearly enrolling didn’t evolve as a defence mechanism because the early, non-complete enrollement forms still allowed access to the softer juicier bits, and also would not have protected against adverse environments either. Neither could its common occurrence be put down to protection against Anomalocaris predation, as it occurs across the range of trilobites, even the itty-bitty ones.

The most obvious reason for enrollment in most, if not all, trilobites after the Cambrian, is that it aided in moulting and not defence, and not defence against Anomalocaris.

But it was the death-knell for Anomalocaris.

Anomalocaris was crucified on the spandrels of San Marco.

Sh*t happens.

Gould, S. J. and Lewontin, R. C., (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique Of The Adaptationist Programme. Proceedings Of The Royal Society of London, Series B, Vol. 205, No. 1161, pp. 581-598.