Oh no! Silence again?

No. I just have family visiting this week and haven't spent much time close to the computer. Instead, I've been guiding half-assed historical tours of Berlin, visiting museums and the aquarium, etc. etc.

I was unaware before yesterday that the Berlin Zoo actuall has a live, captive Tuatara. These poor beasts are on the verge of extinction, something they are often credited with dodging for over 220 million years. That's not exactly true, of course, because modern Sphenodon are not identical to fossil ones, but nevertheless they are the last surviving representatives of that extinct clade.
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"Merck published fake journal"

I've been wanting to blog about this for a while, and it's a story that I don't think should die. Merck is a major pharmaceutical manufacturer who requires no introduction. Elsevier probably requires no introduction to most readers of this blog, but if you are not familiar it is a publishing company that owns an enormous swathe of scientific journals, including top-ranked titles such as Cell and The Lancet. Chances are, if you've done research in science you've linked through the Elsevier or ScienceDirect sites.

According to an article in The Scientist:

Merck paid an undisclosed sum to Elsevier to produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles--most of which presented data favorable to Merck products--that appeared to act solely as marketing tools with no disclosure of company sponsorship.

From the Nature News article

In a statement released on 7 May, Michael Hansen, chief executive officer of Elsevier's Health Sciences Division, acknowledged that, between 2000 and 2005, an Australian office of Elsevier had distributed promotional periodicals that were packaged as journals, without disclaimers clearly marking them as industry-sponsored products.

[...]

During the trial, George Jelinek, a member of the World Association of Medical Editors, testified that the publication would be commonly mistaken for a peer-reviewed journal, even though it was sponsored by Merck and contained only articles that drew positive conclusions about Merck products.

Additionally, the publication listed an "honorary editorial board." One of the listed members, Australian arthritis specialist James Bertouch, reportedly testified that, until recently, he did not know of the journal's existence.

This sort of thing is rather disturbing. To me, it speaks of the dangers of letting a small number of corporations own the bulk of scientific publications. What is equally disturbing is the relative lack of press this story got. This story first appeared in The Scientist and Nature following the report of a lawsuit against Merck. I've seen remarkably little about this elsewhere and it would be a shame if the story died. I'd be interested if anyone could post their own or links to further commentaries about this.
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Oops!

"A treasured piece at the Dutch national museum - a supposed moon rock from the first manned lunar landing - is nothing more than petrified wood, curators say." Full story
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Coming soon...

Here's an interesting project: The Science and Entertainment Exchange. Okay, this is already here, but it will be interesting to know what long-term impact this has on the quality of science portrayal in popular media. Basically, the US National Academy of Sciences is proposing an agency through which to advise entertainment media on portrayal of scientists and scientific matters. An interesting and hopefully fruitful endeavor.

My only concern is that it might end up causing science, as portrayed in the media, to represent the minority of some particular scientists, even if they are members of the National Academy, or are considered 'top' in their field. Oh well, if it can prevent another Mission to Mars disasterpic, then that will right any injustice caused by a mere biased perspective.

(Via Pharyngula)
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A couple of re-posts

Since I've been trying to inject some new life into this blog, I figured I'd link back to some of the few posts that tricked out over the past year or so that might be worth revisiting.

Here are a couple on homology:
Open thread: are genes really a guide homology?

Homology: what's evolution got to do with it?
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A dubious honour...

It seems that my latest paper has been nominated for a dubious honour. That is, I've been singled out as having committed a cardinal sin of systematics: appeals to the reality or significance of paraphyletic groups.

This post was some time ago, and I have not had time to address it. And, I'll mostly not address it in detail here as it is not terribly worth it. Mostly, it is a kind of juvenile stunt, rather than a serious academic undertaking. However, since the authors Williams & Ebach (with whom I actually agree about much, even with respect to fossils), have ascribed to me ideas I do not actually subscribe to: namely a belief in paraphyletic groups, I'll post a little response here. In fact the point of Brazeau (2009) is to demonstrate that a group that is commonly appealed to in the literature, the "Acanthodii" is, in fact, a non-real group.

Most of Williams & Ebach's gripe with my paper is derived from either a BBC report or a non-specialist, non-technical, non-peer-reviewed interview piece in Nature. I have never used the term "missing link" in my article, nor did I use it in discussions with journalists. In fact, I try as much as possible to disabuse journalists of such popular misconceptions.

No, what is most surprising are the factual errors about my work that Williams and Ebach have made:

What any systemtist should do - re-classify the osteichthyans and chondrichthyans in light of this new evidence. Brazeau is naive to suggest that this discovery will "...not overturn a general consensus about gnathostome interrelationships" If Ptomacanthus is more closely related to chondrichthyans then bang goes the acanthodians. They need to be reclassified along with the chondrichthyans.

This contains several patently wrong statements. The monophyly of the Chondrichthyes and Osteichthyes remains after my analysis, as did their status as each other's extant sister group (which my analysis could hardly have contradicted apart from finding if their respective monophyly is not challenged). That general consensus is not changed by my result, so there is no need to re-classify either osteichthyans or chondrichthyans.

The acanthodians do not all get re-classified with chondrichthyans because, as my results showed, some "acanthodians" are members of the osteichthyan stem. So, we have to reclassify some as chondrichthyans and some as osteichthyans. Something I entirely agree with. Figure 3 of my paper clearly shows where I have placed Ptomacanthus in the group Chondrichthyes and a bunch of other "acanthodians" under Osteichthyes and highlighted in bright colours so that you could see that this is what I already did!

Figure caption: a, Strict consensus trees of the 2,904 shortest trees from the global analysis (left; treelength: 318 steps; consistency index: 0.44; retention index: 0.76; rescaled consistency index: 0.34) and the 30 most parsimonious trees from the endocranial data set (right; treelength: 83 steps; consistency index: 0.64; retention index: 0.85; rescaled consistency index: 0.54). b, Bothriolepis. c, Buchanosteus. d, Tetanopsyrus. e, Ptomacanthus. f, Cladodoides. g, Acanthodes. h, Mimia. Vertical arrow shows position of palatoquadrate-braincase articulation that corresponds to the basipterygoid articulation shown in Fig. 2. Double digits indicate percentage bootstrap support; single digits show Bremer decay indices (when greater than 1). Illustrations are modified from refs 5 and 18 (also see Supplementary Information).

Continuing, Williams & Ebach write:

But rather than saying the obvious, Brazeau descends into evolutionary explanation "... populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes". No it does not reveal anything other than that Ptomacanthus is a chondrichthyan and that acanthodians are paraphyletic!

I did state the obvious. It's in the figure. Look at it. I did not "descend into evolutionary explanation". The nested series of monophyletic groups that imply acanthodian paraphyly actually do provide sequences of character acquisition along the chondrichthyan and osteichthyan stem segments. As Williams & Ebach know well, each monophyletic group is supported by synapomorphies, and those nested groups synapomorphies are simply synonymous with what we call 'sequences of character acquisition'. This is how we make sense of fossils (or any other newly discovered taxon) and the implications fossils have, if any, on further hypotheses of synapomorphy (homology). If it's not the sequences of nested homologies that define monophyletic groups (the groups that matter) then what does? I'm perplexed as to why Williams & Ebach, of all people, would challenge this, since this seems to be their own view. I thought we had accepted and moved beyond disputing the idea that "evolution", when talking about fossils and the unrepeatable past, was only reducible to our best systematic hypotheses. In the quoted statement, that is all it is to me. It seems, perhaps, I wasn't careful enough and Williams & Ebach saw what they wanted to see in it. If so, then I'll take responsibility for my error, but note that my critics are playing fast and loose ascribing ideas to me which I have not explicitly stated.

Finally, they raise the following gripe:

"The study also suggests that some acanthodians are ancestors to all modern jawed vertebrates" (BBC Online, 19 January 2009).
This is false and misleading - the study shows quite the opposite.

Mostly, Williams & Ebach are just being pedantic and annoying, but this is infuriating bullshit. Those are not my words!

My words in the BBC article were:

"This figures in nicely with the emerging idea that acanthodians don't form a group of fishes that are all closely related to each other. Some of these fossils are primitive sharks while others are primitive bony fishes."

Even in the BBC article I state clearly that some are chondrichthyans (though I used the term "sharks" as a shorthand) and others are osteichthyans.

I believe my primary sin in that paper is to refer to terminal taxa as "basal". As I will cover here in another post, this is a problematic use of the term "basal", and one that is infectiously used amongst people who apply systematic methods. Maybe that could net me a Pewter Leprechaun, but if you nominate me on that basis you have to nominate just about anybody who talks about trees these days.

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Blogging back to life

I keep trying to revive this thing, and I keep getting distracted. Just shows you something. I believe in communicating science to the public, but I guess my heart is in doing research... especially right now and this early in my career. Nevertheless, I hope to have a few posts up on what I've been working on and what I've been thinking.

Mostly, however, I've just moved to Berlin where I've taken up a postdoctoral fellowship at the Museum für Naturkunde. Slowly, I learn little bits and pieces of German, too... and enjoy the cheap and tasty beer that can be found here.

The Society of Vertebrate Paleontology Annual Meeting is coming up in September. It will be in Bristol, UK. I'm giving a talk. I think the abstracts are embargoed, so I don't think I can publish details of my talk here, unfortunately. But I'll do so as soon as I can.

I'm in the process of writing a review about a topic that has been done to death. Why write a review, you say? Because, in spite of the number of times it's been done to death, the side that is wrong still hasn't died, apparently. Eek! This is taking up a bit of my time because, as you might expect, it's stalling and stalling... kind of like this blog!

In the meantime, I'm CT-scanning lizards*, legless lizards, and snakes at a micro-CT scanning facility here in Berlin. I'm also in the midst of setting up a breeding colony for geckos. Perhaps as things develop more, I will write a bit more about my current project which (as you might have guessed) is somewhat removed from my previous work on fossil fish.

*OH NO! I just use a paraphyletic group! More on that later.
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Nice fossil, shame about the name...

Poor Darwinius, getting all this attention that it can never possibly live up to. Thankfully, a number of blogs out there are offering good summaries and the straight dope on the significance of the fossil. Just to add another fly in the ointment, I must sadly report that the name may become a problem due to it's being published in an online-only journal.

According to the International Code of Zoological Nomenclature:

Article 8.6 Works produced after 1999 by a method that does not employ printing on paper. For a work produced after 1999 by a method other than printing on paper to be accepted as published within the meaning of the Code, it must contain a statement that copies (in the form in which it is published) have been deposited in at least 5 major publicly accessible libraries which are identified by name in the work itself.

I see no evidence in the original paper that this condition has been met. Thus, under the rules of the ICZN, the name Darwinius may not be considered considered "published".
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Evolutionary gems

Nature is running a little online feature 15 Evolutionary Gems that have been published on its pages over the past 10 years.

One of the interesting things you'll note is the amount of molecular biology appearing in the section on the fossil record. Nevertheless, fossils have given us next to zero molecular data (even what is known is a infinitesimally small proportion of fossils in the fossil record). The reason this is possible is because of the way in which fossils fit into the tree of life: they intercalate into the branches between living branches. Thus, they act as a sort of "control" on how we propose hypotheses of morphological change -- in fact they often tell us all we can know about morphological change.

But there's more to this than just fossils: stories from population-level studies show us how the mechanisms of evolution act. Fossils and gene expression data tell us about patterns, but population studies tell us about evolution at the level of process. How natural selection and other forces act to shape the morphology, physiology, and behaviour of organisms can only be studied in real time, using population-based analyses. The work highlighted by Nature tackles important topics such as the role of natural selection in speciation, co-evolution, and the contingent nature of evolution -- the necessary consideration of phylogenetic history in studying adaptation.

Finally, we marry these two through the study of molecular processes. Mutation, gene regulation, epigenetics, these are all forces that influence the possibilities of evolution. These are the driving forces of diversification, but also the conservative nature of descent with modification. It is a slow and stumbling processes. Nature illuminates these issues by covering gene regulation studies in Galapagos finches, insects, among other worthwhile reads.

My main problem with this piece, however, is the way in which item #13 suggests that there is a fundamentally different macroevolution and microevolution. It attributes perceived large steps in evolution as real and refers to them as "macroevolutionary". This reads to me like saltationism, which seems to be bore strictly out of the argument from ignorance or the assumption that gaps in the fossil record are real. Nevertheless, it's a nice summary and worth checking out.
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The end of the long road. A new beginning.

Friday, 21 November, 2008, I successfully defended my doctoral thesis: "Endocranial Morphology and Phylogeny of Palaeozoic Gnathostomes". I'm no longer a student, I'm now a doctor of philosophy. It's a strange feeling being done, but now you know a bit about why I've been conspicuously absent from posting much in the past year. I've had a lot to do!

My next stop will be a postdoctoral fellowship at the Museum für Naturkunde in Berlin. Hopefully, I'll be able to pick up more blogging in the next few weeks. But first, I think I'm going to have a little holiday. Maybe somewhere sunnier than Sweden, for a change...
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Except was no such fella as Noah...

The problem I have is that I'm sure this isn't a metaphor to him.
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Homology: what's evolution got to do with it?

British palaeontologist Colin Patterson became an unwitting friend of creationism during his career. That misbegotten legacy continues to this day, in misquotations that continue to pop up in creationist literature. Patterson has been widely cited by creationists as some sort of closet creationist who though evolution was a speculative farce. Unfortunately, what has become lost in the maelstrom of attack and counter-attack in the world of creation/evolution apologetics are lessons for both evolutionists and creationists.

If anybody was a skeptic, Patterson was. In the forward to his posthumous second edition of his textbook Evolution, two of his close colleagues wrote: "His favourite critical internalised question was 'how do we know that?': to which he often got the answer 'authority or tradition'--something he respected only after he had explored the evidence for himself". He was notorious for a need to figure things out for himself and endeavoured like no other to never let preconceptions get in the way. Indeed, based on anecdotes of people who knew him, I have learned that "how do you know that?" was not merely internalised, but frequently vocalised in a deep Oxford English from the back of the room.

As a result of Patterson's take-no-prisoners approach to belief and science, he became the champion of some unpopular ideas. Patterson questioned every authority and, in the end, challenged (and I believe overturned) some deeply held beliefs about evolution. More importantly, he overturned some ideas about how we know what we know about evolution. For instance, even as a palaeontologist, he argued strongly that fossils themselves play little (if any) role in the establishment of species relationships. That belief emerged from beliefs about fossils revealing ancestor-descendent relationships, and from prior commitments about transformation.

This is where the creationist and evolutionist misunderstandings commence. Patterson argued that evolutionary theory had no role to play in systematics. To creationists, this is touted as evidence that the theory of evolution has no practical applications and is, indeed, unnecessary in biology. To evolutionists, this is often either ignored, disagreed with, or misunderstood.

But what Patterson showed was that a lot of the pre-Darwinian basis for evolutionary theory had been co-opted or subsumed into evolutionary theory. Ideas that had a pre-evolutionary basis had become drenched in evolutionary pre-conceptions and language. Homology, for instance, had become (and still is for most): shared similarity due to common ancestry. However, if homology is explained by common ancestry, then what is the basis for the inference of common ancestry? Well, as it turns out, homology! Patterson recognized the problem and iterated a definition of homology that took into account the way in which homologies define nested groupings. That is, homology is the relation that defines the ranks in a nested hierarchy.

Homologies are homologies because they define nested groups. They are sets of characters that fall into a series of congruent groupings. Similarity alone isn't enough to justify statements of homology, otherwise, we have no way to distinguish convergence from homology. Many will cite examples such as bird, bad, and pterosaur wings as examples where "fundamental differences" allow us to distinguish homology from non-homology.

But, the reality is that we already know these structures are non-homologous because they appear in distantly related groups. We know they're not homologous because of the distribution of other characters which act as a test of homology. If there were ample character evidence that birds, pterosaurs, and bats were all a tightly related group, we might then explain the differences as specializations of a common ancestral wing. The test, ultimately, is whether these taxa share other important characters in common.

The consequence of Patterson's definition of homology--the relation that defines a monophyletic group--is that evolutionary preconceptions are not necessary. Many evolutionists are uncomfortable with this. There is a sort of pluralistic approach (what I call a 'holistic' approach) to homology assessment that many biologists subscribe to. People argue that as many lines of evidence as possible should be considered. I agree, but the question is, through what filter do we analyze this evidence? Patterson would have answered: "tradition, authority, convenience, or assumptions about evolution". There is actually no need to be uncomfortable with Patterson's approach, which I'm surprised has not become more widely embraced.

The problem, as others had pointed out before Patterson, was that we need a knowledge of phylogeny (or interrelationships) in order to know anything about evolutionary history. In order to make generalizations about how evolution works, we need to know the pattern of descent. However, if our assumptions about evolution feed into our inferences about the pattern of descent, these assumptions become untestable. As a result, Patterson argued that our beliefs about evolution played no role in systematics. It was the task of systematists to uncover the patterns that exist in nature which we choose to explain by evolution and common descent. Patterson's rejection of the role of evolutionary theory in systematics was an attempt to keep the enterprise from decaying into circular argumentation.

So, the lesson for evolutionists should be kept in mind as we are deep into a new age in comparative biology. Genes and proteins can now be sequenced, we can map gene expression to embryos, and study the fate of populations of cells in developing embryos. We must ask ourselves: what beliefs about evolution that we developed before these wonderful advances have we carried with us to the present? And for each of these beliefs have we asked: how do we know that?.
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Open thread: are genes really a guide to homology?

I have been putting this question to some of my colleagues:

What is the value of gene expression data in determining homology of morphological features?

Are genes really important in determining if two structures in two different animals are homologous? If so, why? If not, then what does really matter?

Discuss.
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"It will have been more than worth it"

A nice article in the National Post about the fallout from the rumours that Stephen Hawking might move to the Perimiter Institute in Canada. It winds its way to a nice conclusion about the value of supporting basic research and the careers of promising youn scientists. Although it's clearly written by somebody with some first-hand (or otherwise close) experience with science and academia, I can't find the name of the author on the piece.
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Reader comments: Learning about evolution

A question in the comments prompted me to give a response up here:

[I]s there anyway I could learn about evolution without having an upper level education in biology and whatnot, (I'm a senior in High School)?

Yes! The "catch" (if there is one) is that you will develop an upper level education in biology on the way. You just have to do a lot of reading. Thankfully, there are a number of good books out there that can introduce you to the topic. It is, however, a good idea to have a basic familiarity with biology, particularly genetics and a bit of molecular biology. But, to begin with, the material covered in a high school biology class (or equivalent level of textbook) is a good start. It's important to know, for instance, what an allele is, or the base-pairing of DNA. Also, it's important to understand the relationship between DNA and proteins.

The study of evolution is pretty varied. We can break it down into two major parts:

1) The study of the mechanisms and principles that cause evolutionary change
2) The history of life: the historical record and inferred pattern of changes/transformation

It's important to understand both of these things and they will come from different sources. For instance, basic texts on evolution are pretty weak on paleontology. But paleontology texts will be pretty weak on aspects of evolutionary mechanisms. They're needed to complement each other.

The most important thing, beyond anything, is to understand the evidence for any proposition about evolution. Always ask if the evidence is convincing. If so, why? If not, why not?

Some book recommendations:

A few lay-reader type of books that are really good:

Weiner, J. 1995. The Beak of the Finch. Vintage.

Carroll, S.B. 2005. Endless Forms Most Beautiful. Norton.

Zimmer, C. 1998. At the Water's Edge. Free Press.

Texts on biology and evolutionary biology are always a good and obvious place to start. But my preferred way to do things is to get some basic knowledge set up and start looking at evidence (that's how I learn). Books of any type, age, or scope on zoology, botany, anatomy, palaeontology, are very good because they're extremely visual and give you an understanding of the diversity of living form. If you're a very visual learning, as I am, then these can really be helpful. But they're also useful because a lot of texts on evolution or biology talk about things as though they're somewhat divorced from the actual organism to which they might be relevant. A good background in zoology, botany, as well as palaeontology will be extremely helpful.

The short answer is: yes, there are a lot of readily available resources for self-educating in evolutionary biology. Have fun!
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Define evolution in one sentence!

Here's my stab at the challenge:

Evolution is the accumulation of changes over generations in a self-replicating system caused by heritable biases in the probability of self-replication.

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Episode IV: A New Pope

This made my day...


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Being wrong for all the right reasons.

Just a bit of a ramble with some totally unresearched ideas here. Well, not totally unresearched, but impressions and the like, but without explicit references.

Working with fossils can be as frustrating as it is rewarding. It's a lot of fun, but each fossil only tells you so little. In fact, a fossil might be said to really tell you nothing. By themselves, fossils are dry bones, unanimated. Everything we know about fossils depends on our interpretations of them. This seems a little nihilistic, not to mention ripe for creationist misquotation. I'll warn now that there is nothing of use to the creationist here. I'm not talking about the big picture about evolution. I'm talking about the finer points. The crossed t's and dotted i's. Creationists might claim that there are no transitional fossils and try to use my words as a way of showing that even I, the palaeontology graduate student, thinks there's a problem. However, I'm not only predicating this post on the reality that there are many transitional fossils, but that our human frailties might even be preventing us from recognizing more transitional fossils than we have. I believe that we can cut the story of early vertebrate evolution even more finely than most palaeontologists are willing to admit.

When studying the fossil record, we need to recognize patterns. Humans recognizing patterns is tricky business -- we're pattern-seeking animals. We see shapes in the clouds or in random scattering of pebbles in a riverbed. We are often very prone to error, as our common sense thinking can fail us when more arcane matters are in question. We have confirmation bias, where we easily remember the confirming instances for our pet hypothesis but ignore, discard, reject, or rationalise any contradictory observations.

But this is why we have science. The idealised scientist aims to eliminate bias, tries to suspend wishful thinking, and (most importantly) challenges conventional wisdom and common sense thinking. The greatest discoveries in science were not the confirmations of things we already believed, but the revelation the startling facts that were totally inaccessible to our naked perceptions--often demonstrating how wrong we actually were.

There is apparently a world that exists independently of our ability to perceive it. And so, there are necessarily truths about the world that we may not be comfortable with. The point is that science can only tell us something new if it doesn't exist to support those comforting narratives we tell ourselves about how the world works. It is an "unnatural way of thinking" as the embryologist Lewis Wolpert put it:

[T]o do science it is necessary to be rigorous and to break out of many of the modes of thought imposed by the natural thinking associated with ‘common sense’. p. xiii-xiv. Wolpert, L. 1993. The Unnatural Nature of Science. Faber & Faber, Ltd. London

What Wolpert is saying is that science is almost like an affront to a very sacred sense of understanding the world: common sense. It forces us to think in ways that sometimes feel counterproductive, uncomfortable, and even revealing conclusions that do not look like they make sense. The conclusions might be very difficult (or even impossible) to understand.

Palaeontology has, for a long time, been a discipline of narratives. Stories, of whatever sort, tied to fossils in order to explain the patterns observed. The tradition has often been one of very elegant, if not fanciful, speculation that has, in some way, been tied to peculiar observations about fossils. No one can count the speculative hypotheses on dinosaur behaviour, for instance. Some have proven more testable than others, of course. The stories of evolutionary relationships between fossil species, as well as between fossil and living species, were at one time unverfiable just-so stories. At least this was the case in terms of their expression as narratives. We understood two things to be related because they bore homologous structures, but we also knew two things to be homologous because they were borne in related creatures. The cladistic revolution changed that and allowed us to express homology in terms of the nested distribution of similarities. It be came an explicit way of uncovering the patterns in our observations about fossils.

Palaeontology is still experiencing its growing pains in becoming a mature, accountable, rigorous science. The tools, like cladistics and related methods, are there and so is the ambition to use them. However, the steps towards Wolpert's vision of a science are not complete.

Cladistics, when treated with care and in an honest attempt to eliminate your bias, can be very helpful. However, it can just as easily be used to come up with a tree that makes you feel comfortable. It's just an algorithm. You can shove whatever you want in to make whatever you want happen. The point is what the algorithm does, and the logic behind choosing to apply it.

I won't go into the details of it, because I don't think that's what this rant is about. The point is that it acts like a filter for our observations. We can record apparent similarities between a bunch of fossil, or living, or fossil and living things and interpret, in our own minds, what that means. Or, we can subject it to a particular type of analysis that might not give us what our brain tells us it should be. What it will (hopefully) give us is a result of the kind we want, based on logical principles that we have worked out beforehand. These arguments are, themselves, worked out based on some general principles.

Methods like cladistics might not give us the right result. Methods will, at one time or another and however frequently or infrequently fail. Usually for some reason (the method is bad, we used it improperly, or just pure randomness).

The point, interestingly, isn't even about the right answer. It's actually about the wrong answer. We can and will be wrong when trying to explain the world. But we can be wrong for two reasons: the right reasons and the wrong reasons. It's like anything else, you can have all the calculations and the protocols and experimental controls right, and still Nature can throw you a curveball. Or it can be impossible to collect all the neccessary data, or simply impossible to know how much to collect. Nevertheless, we have to try. This can lead to us being wrong, but we will be wrong at no fault of our own. Alternatively, we can be too caught up with getting a result -- especially the result we want. This leads to us being wrong for all the wrong reasons.

So, for those of us working with fossils, I think we can be wrong for the righ reasons and wrong for the wrong reasons. I think honest attempts to challenge received wisdom, to upset old taxonomies, and question the authority of old is a good thing. It may lead us to stronger hypotheses, if not simply to a more honest evaluation of our data. It might be that we simply don't have the evidence to say all the things we're saying. We might, for the time being, only have the evidence for a very coarse picture of interrelationships of some fossil organisms. But the more we strive for a result, and the more we strive for a result that makes us feel comfortable, the farther our thinking get from Wolpert's description of true scientific thinking.
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The origin of whales and "missing links"

The remains of a very basal member of the whale lineage was described this week in Nature. Carl Zimmer's got the gist of it, and you can see pics at Pharyngula. In short, this new fossil material suggests that an aquatic mode of life evolved in the whale lineage at some considerably earlier stage than their predatory mode. The finding is interesting because it illuminates some of the earliest stages in whale evolution.

But at times like this, the term "missing link" likes to fly around in the popular media (but certainly not in Carl Zimmer's writing!). "Missing link" has a certain seductive quality in that it's a familiar concept and can be used to easily grab the interest of lay readership. But therein lies the problem: this does nothing to dispel the misleading notions carried with the term "missing link", and instead only perpetuates them.

As others have pointed out, I'm sure, evolution is not viewed as a chain or a ladder, and concepts that apply such linearity are definitely misleading. However, one could defend the term by nothing that, often times, a fossil might alter the grouping we make and thus "link" one group to another group -- something we didn't know before. But even if that is the case (and it rarely is), no single fossil holds a privileged place in illuminating the tree of life. We understand the importance of a fossil, such as Indohyus, because of what it shares in common (or doesn't share in common) with other fossil forms and other living taxa as well.

Indeed, these forms to which we often apply the label "missing link" do demonstrate structures and charicter combinations that are in some sense intermediate between groups as we recognise them, but that is somewhat misleading as well. For instance, Tiktaalik is widely regarded as a "fish-tetrapod intermediate". In a sense this is true, but it implies the reality of fish as distinct from tetrapods and that one animal somehow bridges this otherwise un-crossable boundary between types. Instead, we understand tetrapods as nested within the bony fishes, with the lobe-finned fishes sharing a special common grouping with them. Among these lobe-finned fishes exists a range of forms that are either more or less like tetrapods than others.

It is within this comparative context that transitions are understood. Sequences of character change are built up be recognizing the common features shared among groups in a hierarchy. It is thus a branching picture, rather than a straight chain with some missing links. The so-called "missing links" get portrayed as somehow essential to the whole story, the last piece of evidence required to prove some otherwise incomplete notion. In reality what they do is quite often to fit neatly into a picture that we already understand very well and serve instead to make the details much clearer.

In the case of Indohyus, it adds important new information in understanding the origin of whales, both from a phylogenetic perspective, but mostly from a functional and ecological perspective. It's not so much a "missing link" no longer missing, as a piece of the puzzle that helps us decide between competing solutions.
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Science as a process: placoderm muscles revisited

You might recall the discovery of fossil placoderms with preserved muscle tissue from earlier this year. I posted on it here, but noted that there was a problem with the analysis, but I didn't say exactly what. This week, the journal Biology Letters published a comment on this paper by a colleague and myself, along with the response from the authors of the original paper.

It's tempting to write a counter rebuttal here, but I'll just let you read the papers if you have access to them. The point is, this is how science works: we depend on other workers being willing and able to criticise our work when they think there is reason to do so. Because of this, science maintains its credibility and its integrity. A case example for your edification. Enjoy.
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