Comments for Buried Treasure

Comment on Commentary: Summarizing papers as word clouds by i9606

i9606 — Mon, 30 Jun 2008 17:14:13 +0000

I was also impressed by wordle, its very pretty. Here is one of my papers tagified. Out lab built a few, now somewhat aging, tools for generating tag clouds for things like query responses to pubmed and connotea and information about proteins in ihop. Perhaps you will find them entertaining.

Comment on Commentary: Summarizing papers as word clouds by Lars Juhl Jensen

Lars Juhl Jensen — Sat, 28 Jun 2008 06:19:05 +0000

I also did not find a way to fetch Wordle images automatically.

Comment on Commentary: Summarizing papers as word clouds by pedrobeltrao

pedrobeltrao — Fri, 27 Jun 2008 18:38:49 +0000

Did you find a way to retrieve the images automatically ? I tried using it to represent authors or labs. Take the last few abstracts from a group to visualize re-occurring themes. It could be nice to put on the lab webpage but I read somewhere that the code was not available and I did not find a way to get it automatically.

Comment on Commentary: Summarizing papers as word clouds by Lars Juhl Jensen

Lars Juhl Jensen — Fri, 27 Jun 2008 12:47:14 +0000

Good idea! The word clouds could be simplified by stemming the words and possibly also by merging autographic variants (e.g. “cell-cycle” and “cell cycle”).

Comment on Commentary: Summarizing papers as word clouds by spitshine

spitshine — Fri, 27 Jun 2008 12:40:54 +0000

You could add stemming too, “proteins” and “protein” should be the same, shouldn’t they? Actually, the third paper comes out quite OK from my point of view.

Comment on Analysis: Cell-cycle-regulated genes encode short-lived proteins by Analysis: Degradation signals correlate with protein half-life « Buried Treasure

Mon, 16 Jun 2008 17:56:00 +0000

[...] License « Analysis: Cell-cycle-regulated genes encode short-lived proteins [...]

Comment on Editorial: Live blogging - not so easy by Lars Juhl Jensen

Lars Juhl Jensen — Fri, 13 Jun 2008 21:16:59 +0000

I was also thinking about buying an Asus Eee PC for a while, but I dropped that idea after trying the keyboard. It is too small for touch typing and too large for thumb typing, which leaves “hunt and peck” as the only viable option.

Instead, I now consider the MSI Wind and/or the Nokia N810. The former has a 10″ display and a keyboard that is large enough to allow touch typing. The latter fits in a (large) pocket and has a 4.1″ screen and a thumb keyboard. Since they can both run Firefox, I hope that all the web interfaces will work properly.

Comment on Editorial: Live blogging - not so easy by scilib

scilib — Fri, 13 Jun 2008 20:00:14 +0000

I’ve found that my Nokia N82 cellphone is good for “liveflickring” since it has a reasonable camera and built-in WiFi and Flickr upload software. I do have a keyboard for it but I’ve found the cellphone blogging applications are just not powerful enough and reliable enough for what I want to do in a quick liveblog. So far I’ve used my 12″ PowerBook for conference blogging, but I’m thinking about trying an Asus Eee 7″ Windows XP laptop. I think the PowerBook may still be the winner due to having a full keyboard plus the fact I have two batteries for it.

There’s some info on my N82 blogging experimentation at http://scilib.typepad.com/techreviews/2008/03/nokia-n82-with.html

Comment on Commentary: Does size matter? by Lars Juhl Jensen

Lars Juhl Jensen — Wed, 07 May 2008 11:04:41 +0000

The standard deviation (and hence the variance) has also increased: it was 4.8 in 1950 and 5.3 in 2008. However, it has increased less than the mean, so the relative standard deviation has decreased from 0.56 in 1950 to 0.42 in 2008.

Comment on Commentary: Does size matter? by rolandkrause

rolandkrause — Wed, 07 May 2008 08:33:56 +0000

Hmm, I wonder whether the variance has decreased of the years and that title lengths reached some consistency.

Comment on Commentary: Colonization of titles by Commentary: Does size matter? « Buried Treasure

Commentary: Does size matter? « Buried Treasure — Tue, 06 May 2008 20:38:32 +0000

[...] License « Commentary: Colonization of titles [...]

Comment on Commentary: Colonization of titles by Answering questions « A Man With A Ph.D.

Answering questions « A Man With A Ph.D. — Wed, 23 Apr 2008 20:43:22 +0000

[...] April 23, 2008 — Richard by Jef Poskanzer Commentary: Colonization of titles: [Via Buried Treasure] You have probably noticed that a high fraction of scientific papers have [...]

Comment on Commentary: Colonization of titles by Lars Juhl Jensen

Lars Juhl Jensen — Tue, 22 Apr 2008 09:34:48 +0000

Guilty as charged ;-) I should mention though that many of my papers with colonized titles are publications in the NAR special issues where the “YADB: yet another database” style is explicitly requested by the publisher.

Comment on Commentary: Colonization of titles by mywordpressname

mywordpressname — Tue, 22 Apr 2008 09:13:47 +0000

Funny, a search in Pubmed for Jensen LJ puts you at the top of the curve. It was a bit tough to discern which articles were definitely yours - but I’d guestimate your use of colons at about 24%.

Comment on Commentary: We apologize by Commentary: Colonization of titles « Buried Treasure

Commentary: Colonization of titles « Buried Treasure — Tue, 22 Apr 2008 06:25:22 +0000

[...] from 15% to 24% over the past 20 years. One could object that this effect may be explained by the increase in apologies (which often have a title “Retraction: …”) or by the NAR special issues on [...]

Comment on Analysis: Cancer or not, cell-cycle expression stays the same by Analysis: Cell-cycle expression of cancer genes « Buried Treasure

Analysis: Cell-cycle expression of cancer genes « Buried Treasure — Tue, 15 Apr 2008 19:58:45 +0000

[...] Yokofakun « Analysis: Cancer or not, cell-cycle expression stays the same [...]

Comment on Commentary: Viewing the cell cycle in a new light by Random Stuff, April 08 « Suicyte Notes

Random Stuff, April 08 « Suicyte Notes — Sun, 06 Apr 2008 22:32:10 +0000

[...] protein ubiquitination for visualizing the cell cycle stage of cells in vivo. Lars Juhl Jensen at Buried Treasure has also picked up this story, and those two blogs provide a lot of detail on the method, including [...]

Comment on Commentary: We apologize by Doubling every 3 years « A Man With A Ph.D.

Doubling every 3 years « A Man With A Ph.D. — Wed, 02 Apr 2008 15:56:54 +0000

[...] every 3 years April 2, 2008 — Richard by josef.stuefer Commentary: We apologize: [Via Buried Treasure] Attila Chordash over at “PIMM - Partial immortalization” discovered that [...]

Comment on Commentary: Much ado about alignments by Lars Juhl Jensen

Lars Juhl Jensen — Mon, 31 Mar 2008 17:07:25 +0000

I see that this post has made it to Genome Technology Online (GTO). I think a small clarification is in place: contrary to what is written on GTO, the six steps do not as such aim to solve the problem. Yes, some of the alignments that gave rise to inconsistent trees before may fixed by running Gblocks. But the real purpose of the analysis I propose is to find out if the inconsistent trees were already known to be unreliable based on bootstrap analysis, or if we have nasty surprises in the sense that even trees with good bootstrap support may be inconsistent with each other.

Comment on Editorial: Live blogging - not so easy by Lars Juhl Jensen

Lars Juhl Jensen — Mon, 31 Mar 2008 07:49:07 +0000

It would obviously be better if everyone uploaded their posters to some site as you suggest. To start with, the graphics quality would be better than what anyone would ever be able to produce with a camera. The problem are that it requires that the conference organizers take the initiative to do so, and that it requires additional work on behalf of the poster presenter.

For the past couple of years, I have always used a digital camera to capture fully readable versions of the posters that caught my interest and emailed some of them to my colleagues when I got back. The photography side of things is thus already routine to me. Trying to blog about each of them while at the poster session would not be realistic. That is why I am looking for a solution that would allow me to immediately post pictures online with a minimum of extra work for me. If I can find that, then I think that live coverage from poster sessions is practical - otherwise, I have to agree with you that it would be really impractical. Which is why I didn’t do it so far ;-)

Comment on Editorial: Live blogging - not so easy by nsaunders

nsaunders — Mon, 31 Mar 2008 01:16:14 +0000

I like the idea of live blogging posters - it would be an interesting, personal record of those posters that interested the blogger - but it sounds really impractical.

Maybe a better solution would be for conferences to require that posters be submitted in digital form, so they can be made available on the web. Or encourage people to upload their posters to a community website such as slideshare or eposters. You could then at least make a live note and link to the resource later.

Comment on Live: Evolution of biological pathways by Lars Juhl Jensen

Lars Juhl Jensen — Wed, 26 Mar 2008 19:12:22 +0000

I fully agree. As much as I liked this work, it is still only evolution of toy models. It would be really cool if one could bring together molecular detail, mathematical modeling, and population genetics in one framework.

Comment on Live: Evolution of biological pathways by pedrobeltrao

pedrobeltrao — Wed, 26 Mar 2008 18:52:46 +0000

Cool work. I still think that a good research direction for this type of work should be to inject more biological details into the simulations. It would make them slower but it would allow bridging molecular properties with circuits and phenotypes.

Comment on Live: Bioinformatics for Molecular Biologists by Lars Juhl Jensen

Lars Juhl Jensen — Wed, 26 Mar 2008 18:45:13 +0000

I’m already back from the meeting. Unfortunately, I did not manage to live blog as much as I wanted - I hate when work interferes with my blogging ;-)

You can find quite a few pictures from the meeting in the Picasa album (just click the picture in the sidebar to get there). You can find the course program at the EuroGene web site (http://www.eurogene.org/). I also have most of the presentations, so drop me an email if you are interested in some of them in particular.

Comment on Live: Bioinformatics for Molecular Biologists by krishnbhakt

krishnbhakt — Wed, 26 Mar 2008 13:57:00 +0000

Will you be posting the lecture online? It will be very interesting for me.

Comment on Update: Warda and Han, one month after the storm by Lars Juhl Jensen

Lars Juhl Jensen — Sun, 16 Mar 2008 11:05:27 +0000

Thanks for the encouragement and sorry about the slow moderation of comments - I am traveling and have only sporadic internet access.

Concerning banning the reviewers, I think we first need to know if the weirdness was at all in a version that was seen by the reviewers. It may easily be that the intelligent design parts were introduced during revision, in which case the revised version may have been accepted by the editor without re-review. The reviewers could thus be completely innocent.

Comment on Update: Warda and Han, one month after the storm by vhedwig

vhedwig — Fri, 14 Mar 2008 18:24:47 +0000

Keep up the pressure! Dunn has essentially ignored all requests to provide more detail, and I think he’s secretly hoping this will all just go away.

The key question is this… have the reviewers been banned from reviewing for this journal ever again? In addition, what will be done to restore confidence in the journal? Dunn and possibly others need to either resign, or do a much better job of explaining why they should be allowed to stay.

Comment on Update: Warda and Han, one month after the storm by Peer blogging the question marks of the Warda-Han paper’s peer review « Pimm - Partial immortalization

Wed, 12 Mar 2008 16:37:40 +0000

[...] Buried Treasure by Lars Juhl Jensen: Update: Warda and Han, one month after the storm [...]

Comment on Editorial: One month anniversary by Pawel Szczesny

Pawel Szczesny — Thu, 06 Mar 2008 18:18:28 +0000

Buried Treasure is certainly worthwhile reading :). Congratulations on this very good start and I hope to comment on your next anniversary in 11 months.

Comment on Commentary: Does just-in-time assembly of protein complexes explain phenotypes? by Analysis: Cell-cycle phenotypes and regulation, part 2 « Buried Treasure

Analysis: Cell-cycle phenotypes and regulation, part 2 « Buried Treasure — Sun, 02 Mar 2008 18:48:28 +0000

[...] blogged about the relationship between cell-cycle phenotypes and regulation in human as well as budding yeast. I was thus excited to see the new RNAi study on cell-cycle phenotypes by Rines and coworkers that [...]

Comment on Resource: The BuzzCloud visualization of buzzwords by Lars Juhl Jensen

Lars Juhl Jensen — Sat, 01 Mar 2008 07:58:36 +0000

I have been thinking about doing some statistics on publications from different countries, but I doubt that it would work in case of BuzzClouds. The problem is one of signal-to-noise: to find fresh new buzzwords, I have to detect them as soon as the first few instances appear in Medline. If I were to geographically subdivide these already low counts, there would be no statistical power left. However, it could be interesting to analyze the usage of already established buzzwords in different countries.

Comment on Resource: The BuzzCloud visualization of buzzwords by bgaeta

bgaeta — Sat, 01 Mar 2008 00:30:42 +0000

It would be fun to do this on a country by country basis as well. I am wondering if there are differences/delays in buzzword “adoption” between countries. For example, I suspect that “biodiversity” and “biodiversity informatics” would be more prominent in Australia than in the US, but many other buzzwords would rise to prominence in Australia a year or two after the US.

Comment on Analysis: Cell-cycle phenotypes and regulation by Analysis: Cell-cycle phenotypes and regulation, part 2 « Buried Treasure

Analysis: Cell-cycle phenotypes and regulation, part 2 « Buried Treasure — Thu, 28 Feb 2008 13:27:21 +0000

[...] Analysis: Cell-cycle phenotypes and regulation [...]

Comment on Commentary: Neither buried nor treasure by Post-vacation random picks « What You’re Doing Is Rather Desperate

Post-vacation random picks « What You’re Doing Is Rather Desperate — Mon, 18 Feb 2008 01:43:46 +0000

[...] new computational biology blog from Lars Jensen - Buried Treasure, via Roland. Lars has written a nice summary of the increasingly infamous mitochondrial ID paper which we were alerted to by [...]

Comment on Commentary: Neither buried nor treasure by Commentary: We apologize « Buried Treasure

Commentary: We apologize « Buried Treasure — Sun, 17 Feb 2008 20:01:50 +0000

[...] Commentary: Neither buried nor treasure [...]

Comment on Analysis: The law of diminishing returns by Commentary: We apologize « Buried Treasure

Commentary: We apologize « Buried Treasure — Sun, 17 Feb 2008 19:57:39 +0000

[...] Analysis: The law of diminishing returns [...]

Comment on Analysis: The law of diminishing returns by rodinsky

rodinsky — Thu, 14 Feb 2008 10:07:18 +0000

Thank you Lars, for following on my comment.
Answering your last question, I personally dislike the use of statistics. Not of the science of statistics, but of statistics that resume data into a number. So I would just plot the distributions of the number of papers per author every five years or so. Also, it would be interesting to see the share of papers per author (for each author, the number of papers published over the number of authors in that paper).
However, the point you made about names is serious and makes the whole exercise doubtful. We could assume that there is more overlap of names now than before, as you did above. In what regards the distributions, if we see that the amount of people publishing little has increased, even with the name bias, we should be able to conclude that there is definitely a lot of authors that before were probably not making it to the author’s list, or that there is a higher turnover of scientific staff.
Another interesting point would be to see the impact of the difference in distributions in your results. To what extent do they justify your findings?
Let’s think about this…

Best regards,

Rodrigo

Comment on Commentary: Does just-in-time assembly of protein complexes explain phenotypes? by Analysis: Cell-cycle phenotypes and regulation « Buried Treasure

Analysis: Cell-cycle phenotypes and regulation « Buried Treasure — Thu, 14 Feb 2008 07:17:46 +0000

[...] Commentary: Does just-in-time assembly of protein complexes explain phenotypes? [...]

Comment on Update: Not treasure but buried by Commentary: Neither buried nor treasure « Buried Treasure

Commentary: Neither buried nor treasure « Buried Treasure — Wed, 13 Feb 2008 07:29:54 +0000

[...] Update: Not treasure but buried [...]

Comment on Commentary: Neither buried nor treasure by Screenshot of the day: Warda-Han-Still-Missing-Link paper retracted! « Pimm - Partial immortalization

Tue, 12 Feb 2008 21:16:15 +0000

[...] of all: thanks to the commenters/scientists (the online flash mobbers) for being the most efficient part of the science blogosphere! Although the paper was retracted [...]

Comment on Analysis: The law of diminishing returns by Lars Juhl Jensen

Lars Juhl Jensen — Tue, 12 Feb 2008 16:15:44 +0000

I have looked at the distribution of authorships, but there is a problem: in 2007 there were 9908 paper published by Wang Y, 8642 by Zhang Y, 8140 by Li Y and 8122 by Wang J etc. The problem is obviously that there are many authors with identical names. And just for the record: all the top-50 names in 2007 are asian.

The first question is how this affects the statistical results I presented in the post. The pooling of authors with the same name will cause me to underestimate the number of active authors per year. This alone will cause me to underestimate the growth in the number of authors as the fraction of authors that become pooled will increase with the number of authors. This effect is further enhanced by demographic changes. Since this does not affect the number of papers published, it thus means that I have underestimated the decrease in productivity (as measured in terms of papers published per active researcher). The general conclusions thus stay unchanged.

Unfortunately, this affects distribution of authorships in a very bad way, which means that measuring the standard deviation of the distribution as suggested by rodinsky will not work. The obvious solution would be to instead use a measure that is robust to outliers (e.g. Zhang Y) such as the median absolute deviation. However, that will also not work. Because more than half of the authors have published exactly 1 paper in a given year, the median becomes 1 and the median average deviation becomes 0.

Any suggestions for how to work around this problem?

Comment on Analysis: The law of diminishing returns by Lars Juhl Jensen

Lars Juhl Jensen — Tue, 12 Feb 2008 12:44:49 +0000

Very good point that everyone makes it onto papers in a more democratic fashion now than earlier (which is obviously a good thing). Especially, I think that lab technicians were generally always left out in the old days, whereas it has now become more common to include them on the author list of experimental papers. Actually, a colleague suggested this to me when I showed him the plots, but I forgot about it when I wrote the blog post.

Comment on Analysis: The law of diminishing returns by rodinsky

rodinsky — Tue, 12 Feb 2008 12:34:38 +0000

Hi Lars,

Nice blog! And interesting finding that there are less papers per author.

Can I come up with one more hypothesis for why the number of authors increases more than papers per author?:

People now work in big groups in which there are a few creative minds and a lot of manual labour and temporary work (like doing a PhD before leaving to industry, etc.). Thereby the productivity of scientific workers might have become more polarized. As well, now everyone makes it to the author list, in a more democratic fashion. If this scenario holds, one would expect the shape of the distribution of authorships also changing, to increased variability (a lot more people with few papers). So you could check this hypothesis…
I dont think that we are left with the hard questions and that the easy ones have been answered. 30 years is a drop of water in the ocean of the scientific unknown…
Best!

Comment on Commentary: Neither buried nor treasure by Update: Not treasure but buried « Buried Treasure

Update: Not treasure but buried « Buried Treasure — Tue, 12 Feb 2008 12:24:42 +0000

[...] Commentary: Neither buried nor treasure [...]

Comment on Commentary: Neither buried nor treasure by pedrobeltrao

pedrobeltrao — Sun, 10 Feb 2008 19:23:55 +0000

wow ! “mighty creator” ?! Very amazing how the editor/referees let this go through. I hope it gets retracted.

Comment on Commentary: Neither buried nor treasure by speechless « Coffee and Sci(ence)

speechless « Coffee and Sci(ence) — Sun, 10 Feb 2008 19:03:17 +0000

[...] borrowing this line from Lars Juhl Jensen, to describe my current status in front of that [...]

Comment on Editorial: Why “Buried Treasure”? by Pawel Szczesny

Pawel Szczesny — Sat, 09 Feb 2008 07:39:11 +0000

I’m looking forward to see more of your buried treasures. Best wishes and good luck!

Comment on Editorial: Why “Buried Treasure”? by pedrobeltrao

pedrobeltrao — Fri, 08 Feb 2008 20:30:15 +0000

Cool to see you blogging and hopefully gain from your contributions. All the best for you blog experiment.