So, what's been happening in the past few days (weeks?) since I last posted? Well, autumn is setting in here, so it's not like I'm spending a lot of time outside right now. I've been focused pretty much on a few things: writing a manuscript, updating a dataset, writing a job application, and learning some programming skills.
One of the nice things about being a postdoc is the flexibility of your time. It is an important period in the life of a researcher where you not only apply those skills you already learned towards being productive, but you have the opportunity to learn new ones. I'm picking up where I left off early in my postgraduate education, learning new tools and tricks for the software environment R. This really is an indispensable tool for biologists, or anyone who applies statistics. I would hope that in the near future, R will become an integral part of undergraduate biology curricula. It combines the ability to analyze data with a programming environment.
As much fun as being a postdoc is, I really want a permanent job—a good one, with lots of interaction with enthusiastic and creative students. Being a postdoc can be limiting, too. There are lots of small cash funds for Ph.D. research projects from various scientific societies, institutions, or funding agencies. I've had a lot of success with these as a Ph.D. student, and I really think they are important in helping students b. On the other hand, faculty tend to operating grants: a fund that supports their research throughout the year or several years. Somewhere in the middle is the postdoc, who has to rely either on his host's grant (allusions to parasitism here may or may not be intended), or the very few small (and therefore competitive) external sources. Thankfully, my current project can make use of a lot of published data, as well as data existing within our collections at this museum. However, I certainly feel the need to grow and develop something much larger and sustained.
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Showing posts with label science. Show all posts
Showing posts with label science. Show all posts
Thursday, October 22, 2009
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:
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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.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.
[...]
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.
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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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Wednesday, May 20, 2009
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:
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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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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Sunday, March 02, 2008
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:
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.
Read full post
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. LondonWhat 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.
Read full post
Thursday, December 20, 2007
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.
Read full post
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.
Read full post
Thursday, December 06, 2007
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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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.
Read full post
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