Monday, August 31, 2009

"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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Friday, August 28, 2009

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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Thursday, August 27, 2009

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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Wednesday, August 26, 2009

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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Tuesday, August 25, 2009

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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