Thursday, January 29, 2009

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!

Tuesday, January 27, 2009

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.

Red Dwarf is back!

There just might be something to the deity stuff you know, because THE BOYS FROM THE DWARF are back!!!!!!!!!!!!!

There were rumours and announcements last September of some new specials celebrating 21 years of Red Dwarf, for one of the free to air stations in the UK, Dave.

But now it's official and it's happening, and stuff is being done.

There have been persistent rumours of more Dwarf, especially a film, but nothing eventuated. Until now.

Two new specials are currently in production at Shepperton Studios.

More info here and here.

Smeggin' Hell!

All hail the might Dave, hallowed be thy name . . .

Sunday, January 25, 2009

New Scientist - creationist shills

I’ve refrained from commenting on the woeful New Scientist cover because I was so angry, and you shouldn’t post stuff when you are angry.

It’s been a few days, but I’m still angry, and comments by the New Scientist staff in a number of blogs, here, here and here, haven’t made things any better.

It’s clear from the comments that the intent of the cover was to sensationalise the story and sell copies, and that the ways in which the cover could be used against evolution were understood, but they didn’t care.

Good people are fighting long and hard to protect science education from the very real threat of creationist ignorance, and New Scientist hands the creationists a propaganda goldmine (as false as the cover is) that requires no misquoting or taking out of context.

The mealy-mouthed distancing from the cover in the editorial and article not only shows that New Scientist knew exactly what they were doing and how the cover could be used, but is also worthless, as the creationists will not read the editorial or the article, and the school boards, that the creationists will use this cover to attack the teaching of evolution with, will not read the editorial or the article.

So good luck with the new sales tactic of flogging your product on street corners with the hack rags, using their tactics, but I will not be buying New Scientist again. I prefer my science reporting with more journalistic integrity that New Scientist can muster.

But hey, there is a potential revenue stream from this. New Scientist could chase all the creationists that will be using this cover in presentations attacking evolution, and invoke copyright. I don’t know how much that’ll bring in, maybe as much as 30 pieces of silver.

Don’t buy New Scientist. Don’t support those that provide support for creationists.
Support those that are fighting to ensure the integrity of science education. Support the National Center for Science Education.

Saturday, January 24, 2009

More Palaeontologists!

I usually skip this sort of stuff, but this is important people!

Amanda is studying to become a palaeontologist, and as we all know, it is an inescapable truth that the world needs more palaeontologists, and is the opinion of all right-thinking people everywhere.

So go here and vote for Amanda's favourite toy - a Brontosaurus - and help her will some money to go towards her college fees.

Tuesday, January 20, 2009

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 . . .

Ignorance attacks atheist bus sign

And now, in the "I don't think they've thought this through" catagory . . .

A really sad Christian group in the UK, Christian Voice, has complained to the Advertising Standards Authority (ASA) about the atheist signs on buses in London that say "There's probably no God. Now stop worrying and enjoy your life."

The grounds? the signs break the ASA's rules on substantiation and truthfulness!

The ASA's code states "marketers must hold documentary evidence to prove all claims". The regulator said it would assess the complaint and decide whether to contact the advertiser.

There relevent portion of the code is:

marketers must hold documentary evidence to prove all claims.

The regulator is said to it be assessing the complaint and decide whether to contact the advertiser.

A spokesperson for Christian Voice (identity here concealed to protect the stupid) said,

There is plenty of evidence for God, from people's personal experience, to the complexity, interdependence, beauty and design of the natural world.

"But there is scant evidence on the other side, so I think the advertisers are really going to struggle to show their claim is not an exaggeration or inaccurate, as the ASA code puts it.

The British Humanist Association is not worried. Hanne Stinson the chief executive, said: "I am sure that Stephen Green really does think there is a great deal of evidence for a God (though presumably only the one that he believes in), but I pity the ASA if they are going to be expected to rule on the probability of God's existence."

I just have one word:


More from the BBC website.

Monday, January 19, 2009

There's gold in them thar broken pots

I like archaeology. Primarily because I have a good friend who is an archaeologist (hi Gail), and through the excellent "Time Team" program.

Granted, compared with Ediacaran and early Cambrian palaeontology, archaeology is like spashing around in the shallows, but they dig stuff up, so that's OK.

There is news of a big find of late iron age gold coins in a field near Wickham Market, Suffolk, UK, dating from around 2050 BP to 1995 BP. The find consists of 824 gold staters, worth, at the time, the equivalent of around 0.5-1 million pounds. That's a lot of anyone's money! (though, sadly for the finder, they are not worth that now.)

The find, contained in a broken pot, was uncovered in a field by someone using a metal detector. Interestingly, the find was not associated with any major structures, but is though to indicate that this must have been an important economic area during the period.

The record for a find of gold staters was in 1849, when a farm worker found between 800 and 2,000 coins in a field near Milton Keynes.

Sunday, January 18, 2009

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!

Friday, January 16, 2009

What is science?

Larry Moran has an excellent video about the difference between science and superstition. I'm not embedding in here as you should be reading Sandwalk anyway!

Wilkins has his view here.

Thursday, January 15, 2009

Palaeoporn 8

Just your average slab from the Lower Cambrian Emu Bay Shale (click on image to enlarge)! Well, not quite, but a very nice assemblage all in one spot.

First the big trilobite Redlichia takooensis (Red). Two specimens here, but the larger one is pretty much complete. It's a moult though. You can tell it's a moult because the suture lines on the head are disturbed. If you follow the outer margin of the head you will see some points where the edge is not smooth and there is a break, just like a little fault. These are the suture lines, which break to allow the cutilcle to break and the animal to exit through the head end.

This specimen also has a good example of a medial spine. That's the big pointy thing coming out of the back end. It actually attaches to the animal at segment 11 on the thorax (count back from segment 1 at the head end). There is also a spine coming off the head, dead in the middle of the back margin and overlapping the first segment.

The other trilobite common to the Emu Bay Shale is Estangia bilobata (Est), a much smaller trilobite, but actually more common.

The largest feature is, of course, Anomalocaris briggsi (Anom). There are two appendages, again probably moults. See Palaeoporn 1.

The other critter, lying underneath the Anomalocars appendage, is Isoxys communis (Iso). Isoxys is a phyllocarid crustacean, which occurs occasionally in the sequence. They get quite big, with this one being around 5cm not including the spines. Elsewhere (e.g. the Burgess Shale) they are normally get up to 2-3cm.

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! :-)

Wednesday, January 14, 2009

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
Pit image from

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

Tuesday, January 13, 2009

Give 'em the finger

Researchers at the University of Cambridge have compared the success of financial traders with the length of their ring finger compared with the index finger, with some surprising results.

The length of the ring finger is fixed during development in the womb and a ring finger longer than the index finger indicates prolonged exposure to the male hormone androgen.

Researches compared the results of 44 male stock traders involved in rapid decision-making and quck phsical reactions, over 20 months. They found that traders with longer ring fingers made 11 times more money that those with the shortest ring fingers. Of the experienced traders, those with a longer ring finger made 5 times more that those with short ring fingers.

Clearly, this comprehensive, well executed, and important research needs to be widely circulated.



Well, I hadn't checked. Just a minute . . .

Oh, look at that, I have a longer ring finger!

(Hmm, don't know how I'm going to break the news to my twin sister . . .)

John M. Coates, Mark Gurnellc, and Aldo Rustichinid, (2009) Second-to-fourth digit ratio predicts success among high-frequency financial traders. doi:10.1073/pnas.0810907106

Sunday, January 11, 2009

Myoscolex - a Lower Cambrian Opabinid

This is Myoscolex ateles (click on the images to enlarge), a common element of the Emu Bay Shale faunal assemblage – which is a restricted fauna of only some dozen species (this compares with over 150 for the Burgess Shale). Why the Emu Bay Shale is such a restricted fauna will be covered in a future post on fossilisation.

The preservation of Myoscolex is striking. The grey material is calcium phosphate (apatite) and the red material is calcium carbonate (calcite) – in this case the calcite is just a light dusting over the apatite. The material preserved is muscle tissue – one of the earliest examples of phosphatised muscle tissue known. The colours actually pick out the two sets of muscles in the organism. The grey apatite highlights the longitudinal (along the body) muscle bands, while the red area highlights the dorso-ventral (top to bottom) muscle bands.

One feature not present in all specimens are rod-like structures. In the original description of Myoscolex from 1979, these rod-like structures were interpreted as paripodial setae, and the animal classed as a polychaete worm, although it was admitted that the setae were different from any yet known in polychaete worms.

A number of factors, including the collection of more specimens with new information, and a better understanding of soft tissue fossilisation, resulted in a re-evaluation of Myoscolex as part of my work on the Emu Bay Shale.

It was found that Myoscolex is actually quite common, around 15% of all fossils found (trilobites were the most common at just over 50%), and that pretty much all the Myoscolex specimens found were in the same orientation - laterally flattened and straight (as in the first image). This was unusual in polychaetes, who tend to be found dorso-ventrally (top to bottom) flattened, and exhibit a greater range of flexibility.

A close analysis of the rod-like structures showed that they were paired, and extend out from the body itself. Not only that but they were preserved at different levels on the fossil. Check out the second image showing the rods. You can see the pairs, but one rod is missing, with only the imprint of where it was. This indicated that in the fossil, the pair of rods were lying at slightly different levels in the rock. In this instance, the missing rod was slightly higher in the rock and has separated with the upper part of the fossil when the rock split. The fact that the rods extended some distance from the body (as represented by the muscle tissue), and that they are not level, suggests that they have something to do with endoskeletal sternites, or the lower portion of the body segment. Which means that the animal must have come to rest on it's side and then been flattened so that the sternites folded up into a "U" shape with the lateral (outer) edges coming to rest close together like the top of the "U".

Except worms do not have sternites. Hmmm.

Then there was a breakthrough with this single specimen, which showed beautiful appendages.

And they don't look like appendages any worm would have. They are paired and extend a considerable distance from the body of the animal. Plus the appendages differ in their orientation along the body, indicating that they were flexible. This find also explained why almost all the fossils were found in lateral aspect. The appendages would have come together under the animal upon death or burial, with lying on the side the most stable position. The appendages also showed a variation in attitude along the body, indicating a degree of independent flexibility.

This specimen also showed a portion of the tail, which pointed upwards.

These findings alone were enough to re-evaluate the animal, but a specimen with a head turned up, and things got weird.

Nice eyes (E), shame about the number! Wait a minute, 3 eyes?! 3?! Yeah, and they aren't the same either. The two at the top in the specimen are sub-circular, but the one on the bottom is large elongate structure, which could be one long eye, or two or three that are overlapping ue to twisting of the head. The eyes are also preserved differently - as featureless films of fibrous calcite, not apatite, which indicated that there is no muscle tissue involved (as expected in eyes).

Not only that but there is a faint structure running backwards along the bottom of the head and start of the body (P). It's not well preserved, but is formed of apatite which means that it had contained muscle tissue, and is interpreted as a proboscis. Another specimen showing a possible proboscis is shown at right.

So what type of organism has more than two eyes, a proboscis, flappy paddle appendages, and an upwards pointing tail?

Well, the obvious candidate is Opabinia from the Middle Cambrian Burgess Shale. A check of the numerous reconstructions of Opabinia show that the same suite of characters are present, even the change in orientation of the paddle appendages along the body.

So Myoscolex has been reclassified as an arthropod of similar affinities to Opabinia. So Myoscolex is an Opabinid, or maybe Opabinia is a Myosolexid, as Myoscolex is older than Opabinia ;-)

Saturday, January 10, 2009

Venomous mammal

This is just so cool. Video of Solenodon paradoxus, or the Hispaniolan Solenodon, from the jungle of the Dominican Republic. S. paradoxus and S. cubanis (from Cuba) are the only mammals known that can inject venom through specialised teeth.

While no other known living mammal can inject venom in this way, a number of fossil mammals have similarly modified teeth, and so it is though that this ability may have been more widespread in the geological past.

The animal is very rare - although if you looked like an old man with a bad toupee, you'd be reclusive too!

More info in the BBC story that accompanies the video.

Sunday, January 4, 2009

Trouble in paradise

As some of you may know, Ken Ham’s Answers in Genesis in Kentucky has been in litigation with Creation Ministries International (CMI) – the old “Answers in Genesis” in Australia (AiG in Australia was forced to change it’s name over this).

It’s been fun to watch this unfold since 2005, and some interesting documentation has been produced. I will not go into details as information can be found here and here.

The latest salvo was that Answers in Genesis in Kentucky wanted CMI to attend and be bound by “Christian Arbitration” with American-based, Peacemaker Ministries. CMI objected to arbitration in general, saying that many of the issues are to resolved under Australian law, and to Peacemaker Ministries in particular. The judge has ruled that arbitration should take place (a loss for CMI), but that it take place under the American Arbitration Association (a loss for AiG).

That’s where it sits at the moment.

A list of documents relating to the litigation can be found here and it provides some interesting reading.

For example, you’d think this is all about the freedom to operate to spread the word of G-d, right? Well according the attorney for AiG in Kentucky, one of the reasons for a rapid conclusion to the case is:

. . my client is prohibited or impeded from using its name in conjunction with its ministry or any of its materials in any of these English-speaking countries outside of the United States and the U.K. We have a big market presence, have a lot of supporters, and customers, in Australia, New Zealand, and Canada.

We can't do business in these countries pending the cloud on this title.


CMI aggressively goes after churches, ministries, distributors, and retailers that sell anything that have anything to do with my client in Australia, Canada, and New Zealand It hurts my client's business. (p.27)

So there you go, it’s all about the money.

Want more?

One of the documents lists an application by AiG to register Answers in Genesis as a trade mark in Canada.

Hang on. Didn’t their attorney say that, my client is prohibited or impeded from using its name in conjunction with its ministry or any of its materials in any of these English-speaking countries outside of the United States and the U.K.? Hmmm.

Anyhow, Answers in Genesis International which appears to opperate out of the same building in Queensland as CMI), has objected and had introduced an application of it’s own to register Answers in Genesis as a trade mark in Canada.

This is part of what Answers in Genesis in Kentucky want their trade mark to cover:

Pre-recorded video discs containing movies, seminars and lectures in the field of creation science; video game cartridges and software; sunglasses; interactive multimedia computer game program, educational software featuring instruction on material related to creation science; pre-recorded DVDs containing movies, seminars and lectures in the field of creation science; computer screen saver software; pre-recorded compact discs containing music, seminars and lectures in the field of creation science; children's educational software featuring material related to creation science; decorative refrigerator magnets; magnets; wall calendars; trivia cards; trading cards; tracing paper; paper towels; three-ring binders; story books; stories in illustrated form, namely illustrated books in the field of Biblical apologetics; stamp pads and inks; stationery boxes, folders, writing paper, envelopes and stationery-type portfolios; sketch books, pads, and sketches; scrapbooks, albums and pages; religious books; prayer books; pocket calendars; playing cards and cases; pictures; picture books; pens; pencils; paper name badges; paper napkins, paper note tablets; paper party bags; paper plates; paper display boxes, flags, empty gift bags, gift wrap bows, gift wrapping ribbons; identification tags; painting sets for children; paintings, pamphlets; note books; note cards; note pads; notebook paper; notebook dividers; posters; markers; marking pens; lunch bags; letter openers; ink pens; greeting cards; gift cards, gift wrapping paper; fountain pens; flash cards; felt tip markers, pens; engraving plates; engravings; embroidery design patterns; desk calendars; comic books, comic strips; comic strips' comic features in the field of Biblical apologetics; coloring books; children's activity books; children's books; children's story books cartoon prints; cartoon strips; calendar desk pads; calendars; bumper stickers; bookmarks; baby books; ball point pens; arts and craft paint kits; art pictures; art prints; architectural models; squeeze bottles sold empty, glass mugs, drinking glasses, cups, coffee cups, lunch pails, lunch boxes; bath towels, pillow cases, covers, and shams, handkerchiefs, bed sheets, bed spreads; trousers; t-shirts; ties, sweat shirts; sweat pants; sweat bands; sweat shorts; sweat suits; sweaters; swim wear; swim suits; sport shirts; sleep shirts; sleepwear; slippers; scarves; rain boots, clothing, namely, coats, jackets, suits, and rainwear; polo shirts; ponchos; neckwear, namely, neckties, neckerchiefs; knit shirts; hats; gym shorts; gym suits; clothing caps; prerecorded audio cassettes, tapes, video cassettes, and video tapes featuring material related to creation science; children's video tapes featuring material related to creation science; audio cassettes, audio digital tapes, audio compact discs and audio tapes featuring music, seminars and lectures in the field of creation science; printed lectures and seminar notes; printed teaching books and pamphlets and teaching activity guides featuring material related to creation science; newsletters featuring material related to creation science; magazines featuring material related to creation science; educational books featuring material related to creation science; publications, namely training manuals in the field of material related to creation science; brochures featuring material related to creation science; books featuring material related to creation science.

Rain boots!? Rainwear!? Do AiG know something they’re not telling us? There’s not another flood due is there?

Friday, January 2, 2009

Large dinosaur fossil depoit

There’s a story on the BBC news web site about a large find of dinosaur bones in Shandong Province, China.

Chinese scientists are claiming that it is the largest collection of dinosaur bones ever found, with some 7600 bones collected since March.

There isn’t much information, but apparently the finds, from the Late Cretaceous, include tyrannosaurs, ankylosaurs, and the largest duck-billed dinosaur every found.

Since collecting has been going on since March there may be other information out there in the blogosphere.

Thursday, January 1, 2009

PalaeoPorn 7

Dickinsonia rex - Prince of Worms
No. it's not a door mat, this is Dickinsonia rex. As it's name suggests, it is the biggest Dickinsonia species, and this is the biggest specimen ever to have been collected. Click on the image for a full sized version, but before you do, see the white ruler acting as a scale? That's a 12" (30cm) ruler!

The image on the right is a close up of the top half, showing the mid-line gut, and the ornamentation along some of the segments to the right (again, click on the image for the full size version - I've cut the quality of both images as the original files are 3MB and 4MB). The scale is 30cm.

We found 'Dick' while checking out a pristine site. The specimen had eroded out of the low-dipping bedrock and had fragmented and slid down a gentle slope. I found the dark piece (towards the top right) as it was fossil side up (and hence weathered). Ediacaran fossils are usually on the underside on the bed, as the bed represents a mantling sand that covered the organisms and hence they imprinted onto the bed's lower surface. My colleague and Senior Researcher at the time, Richard, realised that - as this was a pristine site - the rest of 'Dick' was probably nearby. So we spent the rest of the day combing an area the size of a tennis court, looking for pieces.

We found most of what you see on the first day, but went back the next day an found a couple of other pieces. The missing piece was found, but the surface had weathered off - just like parts of the dark piece next to it at bottom right - and so we left it.

'Dick' is complete apart from the missing piece. The mess at the bottom is the tail that is folded back on itself.

Total length after folding back the tail 3ft (90cm)
Total width 1ft 8in (55cm)

What you can't see from the images is the thickness of the individual pieces. The bed is around 6" (15cm) thick.

'Dick' shows a number of features, such as a beaver-like tail (not shown well here), a central gut trace, possible elytra or plate-like scales on the segments, and evidence of muscles. But that's for another post.

'Dick' is currently on display at the South Australian Museum.