33 posts · 15,972 views
You've reached the blog of Daniel Ocampo Daza, biologist and PhD student in neuroscience. I started Ego sum Daniel as a place to practice my scientific writing and to some extent to record my experiences as a doctoral student. I primarily blog about evolution, criticism of creationism and other superstitions, neuroscience and sometimes general biological subjects that I find interesting.
Daniel
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- December 1, 2011
- 03:31 PM
- 152 views
Two ways of looking at the same proteins: Insulin-like Growth Factor Binding Proteins
by Daniel in Ego sum Daniel
Back in June I blogged about a research paper that we had just published with myself as the lead author. The subject of our paper was the evolution of the Insulin-like Growth Factor Binding Proteins (IGFBPs), and how this family of proteins has expanded in vertebrate evolution. Yesterday I noticed that this paper, "my" paper!, now has received its very first citation! This was a my first paper as lead author, so naturally I avidly checked it out.
The research paper that cites us is in press ........ Read more »
Nili, M., Mukherjee, A., Shinde, U., David, L., & Rotwein, P. (2011) Defining the disulfide bonds of insulin-like growth factor binding protein-5 by tandem mass spectrometry with electron transfer dissociation and collision induced dissociation. Journal of Biological Chemistry. DOI: 10.1074/jbc.M111.285528
Ocampo Daza D, Sundström G, Bergqvist CA, Duan C, & Larhammar D. (2011) Evolution of the Insulin-Like Growth Factor Binding Protein (IGFBP) Family. Endocrinology, 152(6), 2278-89. PMID: 21505050
- September 29, 2011
- 10:15 AM
- 179 views
Is there anything fish don't do? Tool use!
by Daniel in Ego sum Daniel
This video and story have been making the rounds on the Internet in the last few days. I just saw it yesterday and it's fascinating! For the first time (allegedly), "tool-use" in a fish has been filmed and the behavior is available for all of us to see. The fish in question is a species of wrasse observed in Palau, Choerodon anchorago or orange-dotted tuskfish.
You can see the fish digging out a clam with its pectoral fin, then carrying it over to a rock or a coral head and cracking it with ........ Read more »
Bernardi, G. (2011) The use of tools by wrasses (Labridae). Coral Reefs. DOI: 10.1007/s00338-011-0823-6
Jones, A., Brown, C., & Gardner, S. (2011) Tool use in the tuskfish Choerodon schoenleinii?. Coral Reefs, 30(3), 865-865. DOI: 10.1007/s00338-011-0790-y
- September 8, 2011
- 12:53 PM
- 273 views
Some notes on the Atlantic cod genome, and fish genomes in general
by Daniel in Ego sum Daniel
Teleost fish genome sequences have been absolutely essential to our understanding of vertebrate genome evolution, and to vertebrate evolution in general. Last month I welcomed the addition of the Atlantic cod genome to the sequenced fish genomes, and highlighted some of the main findings of the first analysis of the whole genome sequence. The preliminary genome database is now available for browsing at the Pre!Ensembl database.
After I had written that post, I had some notes left over becaus........ Read more »
Star, B., Nederbragt, A., Jentoft, S., Grimholt, U., Malmstrøm, M., Gregers, T., Rounge, T., Paulsen, J., Solbakken, M., Sharma, A.... (2011) The genome sequence of Atlantic cod reveals a unique immune system. Nature. DOI: 10.1038/nature10342
- August 17, 2011
- 09:59 PM
- 188 views
The "living fossil" discussion and that "living fossil" eel you might have heard of
by Daniel in Ego sum Daniel
I don't like the term "living fossil". Sure, when used well it can be eye-catching in a pedagogical way, but it's still sort of vague and problematic, and used badly it's outright confusing and may reinforce misconceptions about evolution. That's why when you see it used, you often see it between quotation marks followed by an explanation motivating why the organism in question is called a "living fossil" to begin with. Today we learn about the discovery of a really striking and interesting new ........ Read more »
Johnson, G., Ida, H., Sakaue, J., Sado, T., Asahida, T., & Miya, M. (2011) A 'living fossil' eel (Anguilliformes: Protoanguillidae, fam. nov.) from an undersea cave in Palau. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2011.1289
- August 12, 2011
- 05:25 PM
- 314 views
The Atlantic cod genome is available
by Daniel in Ego sum Daniel
Great news for those of us who are interested in comparative genomics, and fish genomes in particular - yesterday the Atlantic cod genome was made public at the cod genome project website to coincide with the description of the genome, published online in advance by Nature (reference below).
I've been pottering about in the genome since yesterday morning, looking for the gene families I'm researching in my own work, but the database is still quite rudimentary and tricky to use. Most of the se........ Read more »
Star, B., Nederbragt, A., Jentoft, S., Grimholt, U., Malmstrøm, M., Gregers, T., Rounge, T., Paulsen, J., Solbakken, M., Sharma, A.... (2011) The genome sequence of Atlantic cod reveals a unique immune system. Nature. DOI: 10.1038/nature10342
- July 31, 2011
- 08:22 PM
- 329 views
Xiaotingia
by Daniel in Ego sum Daniel
The subject of feathered dinosaurs and the evolution of birds is something that fascinates me and captures my imagination, as I'm sure it does a lot of people. Not only because it changes the way we look at the world around us, specifically birds, but also because there's a lot of cool evolutionary science involved in the study of the early evolution of birds from... well, yes that's the question, isn't it? From what exactly? We know that in any evolutionary sense that matters, birds are dinosau........ Read more »
Xu, X., You, H., Du, K., & Han, F. (2011) An Archaeopteryx-like theropod from China and the origin of Avialae. Nature, 475(7357), 465-470. DOI: 10.1038/nature10288
- July 22, 2011
- 08:20 AM
- 369 views
A quick Mendel follow-up
by Daniel in Ego sum Daniel
As a footnote to my previous post about Gregor Mendel, I offer these interesting Google NGrams.
To start off, we plot the terms "Gregor Mendel", just "Mendel", "Mendelian" as well as the genus of the garden pea Mendel worked with, "Pisum".
Not surprisingly, the years 1866 and 1900 (or there around) stand out markedly.
1866 was of course the year Mendel published his paper Experiments in Plant Hybridization, and we can see that mentions of his name, or at least his surname, and mentions of ........ Read more »
Weinstein, A. (1977) How unknown was Mendel's paper?. Journal of the History of Biology, 10(2), 341-364. DOI: 10.1007/BF00572646
Olby, R. (2009) William Bateson's Introduction of Mendelism to England: A Reassessment. The British Journal for the History of Science, 20(04), 399. DOI: 10.1017/S0007087400024201
Lenay C. (2000) Hugo De Vries: from the theory of intracellular pangenesis to the rediscovery of Mendel. Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie, 323(12), 1053-60. PMID: 11147091
- June 30, 2011
- 01:36 PM
- 397 views
The mighty coelacanth
by Daniel in Ego sum Daniel
I've added the above illustration of a Coelacanth (Latimeria chalumnae) to my collection of illustrations together with one I had already made of a lungfish (open image). If you like you can download both high-res TIF-files here. The same Creative Common license applies as described under the "Download Illustrations" tab above.
I was prompted to add the coelacanth after reading a recent fascinating article about the secretive lives of these marvelous fish (via Deep Sea News) by........ Read more »
Fricke, H., Hissmann, K., Froese, R., Schauer, J., Plante, R., & Fricke, S. (2011) The population biology of the living coelacanth studied over 21 years. Marine Biology, 158(7), 1511-1522. DOI: 10.1007/s00227-011-1667-x
- June 27, 2011
- 07:24 PM
- 380 views
Nicotine, appetite and the brain
by Daniel in Ego sum Daniel
Nicotine is not only very, very addictive, as a central nervous system stimulant it can also affect our motivations and behaviors in a wider sense. One of the behaviors it can modify is appetitive behavior. It's a well-funded fact that smokers tend to have a lower body-mass than non-smokers, and that smokers who quit have a tendency to gain weight, although until now the neurobiological mechanism for this modulation was unknown.
Recent findings from two different publications reveal parts........ Read more »
Mineur, Y., Abizaid, A., Rao, Y., Salas, R., DiLeone, R., Gundisch, D., Diano, S., De Biasi, M., Horvath, T., Gao, X.... (2011) Nicotine Decreases Food Intake Through Activation of POMC Neurons. Science, 332(6035), 1330-1332. DOI: 10.1126/science.1201889
Huang, H., Xu, Y., & van den Pol, A. (2011) Nicotine excites hypothalamic arcuate anorexigenic proopiomelanocortin neurons and orexigenic neuropeptide Y neurons: similarities and differences. Journal of Neurophysiology. DOI: 10.1152/jn.00740.2010
- June 7, 2011
- 12:42 PM
- 359 views
IGFBP evolution: An interesting case of gene family expansion and retention
by Daniel in Ego sum Daniel
Or: How I really should have come up with a better title.
A small announcement: I have an article out as a first author in this month's issue of the journal Endocrinology. It's a nice journal and we spent a long time working on the manuscript so I'm very pleased that it's out. Here's a Worlde word cloud of the whole article... pretty interesting. It sums everything up pretty well actually. It's all about the evolution of the Insulin-like Growth Factor Binding Protein fa........ Read more »
Ocampo Daza D, Sundström G, Bergqvist CA, Duan C, & Larhammar D. (2011) Evolution of the Insulin-Like Growth Factor Binding Protein (IGFBP) Family. Endocrinology, 152(6), 2278-89. PMID: 21505050
- June 3, 2011
- 09:38 AM
- 519 views
Turn off the lights and let melatonin run free
by Daniel in Ego sum Daniel
>> I started the following post about melatonin sometime in March to coincide with my lecture on biological rhythms on our undergrad neurobiology course. But I got really busy and then really sick so I never actually finished it. Here it is then at last.
An all too common sight, at least at my place. This is my Mac glaring. But how is our exposure to low-intensity artificial light before bedtime affecting our sleep cycle?
Twice every year I lecture to undergraduate students in biology ........ Read more »
Hardeland, R., Cardinali, D., Srinivasan, V., Spence, D., Brown, G., & Pandi-Perumal, S. (2011) Melatonin—A pleiotropic, orchestrating regulator molecule. Progress in Neurobiology, 93(3), 350-384. DOI: 10.1016/j.pneurobio.2010.12.004
Gooley, J., Chamberlain, K., Smith, K., Khalsa, S., Rajaratnam, S., Van Reen, E., Zeitzer, J., Czeisler, C., & Lockley, S. (2011) Exposure to Room Light before Bedtime Suppresses Melatonin Onset and Shortens Melatonin Duration in Humans. Journal of Clinical Endocrinology , 96(3). DOI: 10.1210/jc.2010-2098
Boivin, D., Duffy, J., Kronauer, R., & Czeisler, C. (1996) Dose-response relationships for resetting of human circadian clock by light. Nature, 379(6565), 540-542. DOI: 10.1038/379540a0
- February 2, 2011
- 10:40 AM
- 365 views
Oxytocin, ethnocentrism and evolution (pt. 2)
by Daniel in Ego sum Daniel
I didn't want to risk making my previous post too long, and I wanted to keep it focused on "hormonal determinism", so I set aside a whole branch of my commentary on the link between the hormone oxytocin and ethnocentrism for another post. The findings I comment on were presented by De Dreu and co-workers in the latest edition of PNAS (see reference below).
So, today I want to talk briefly about bad evolutionary arguments.Continue after the jump »
... Read more »
De Dreu CK, Greer LL, Van Kleef GA, Shalvi S, & Handgraaf MJ. (2011) Oxytocin promotes human ethnocentrism. Proceedings of the National Academy of Sciences of the United States of America, 108(4), 1262-6. PMID: 21220339
- February 1, 2011
- 12:37 PM
- 337 views
Oxytocin, ethnocentrism and "hormonal determinism"
by Daniel in Ego sum Daniel
There is an inordinate readiness, both within scientific circles and in popular scientific understanding, to ascribe direct causation to the actions of hormones, especially when it comes to moods and behaviors. For example, consider how you’d usually interpret the common expression “being hormonal”. I consider the thought that hormones somehow “control” our moods and behaviors a falsehood; a popular misunderstanding or oversimplification that hinders the understanding of what’s actu........ Read more »
De Dreu, C., Greer, L., Van Kleef, G., Shalvi, S., & Handgraaf, M. (2011) Oxytocin promotes human ethnocentrism. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1015316108
De Dreu, C., Greer, L., Handgraaf, M., Shalvi, S., Van Kleef, G., Baas, M., Ten Velden, F., Van Dijk, E., & Feith, S. (2010) The Neuropeptide Oxytocin Regulates Parochial Altruism in Intergroup Conflict Among Humans. Science, 328(5984), 1408-1411. DOI: 10.1126/science.1189047
- December 8, 2010
- 06:12 PM
- 421 views
Falsehoods associated with the arsenic-thriving bacteria story: What it is and what it isn't
by Daniel in Ego sum Daniel
>> My previous post was more of a summary of what the reporting of the "NASA arsenic-thriving bacteria" story looked like from my perspective in the wake of the massive Internet onslaught of information. In this post I want to talk about how the style of communication that drove this story has lead to the dissemination of falsehoods or misconceptions that hinder a proper understanding of biology in general, regardless of the validity of the actual findings.
The aftermath
Last week I conc........ Read more »
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. info:/10.1126/science.1197258
- December 3, 2010
- 06:48 PM
- 424 views
My summary of NASA's arsenic-thriving bacteria story
by Daniel in Ego sum Daniel
Almost instantly after coming home from work yesterday, I noticed a steady stream of mentions of a mysterious and hugely hyped NASA press conference scheduled for later in the day trickling in via Facebook, Twitter, blogs and news sites. I got excited, but also a bit confused. NASA's announcement seemed spectacular enough:
NASA will hold a news conference at 11 a.m. PST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life.
Af........ Read more »
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. info:/10.1126/science.1197258
- November 18, 2010
- 12:51 PM
- 399 views
Is there anything fish don't do!? Mucus-feeding and prolactin
by Daniel in Ego sum Daniel
Much of my work involves studying fish genomes. Over time I've gotten to know them pretty well and I can only conclude that fish are incredible and inordinately interesting creatures. Unfortunately fish have an undeservedly low standing in the eyes of the general public, as well as many researchers in more mammal-oriented fields, often being referred to as "lower vertebrates" in the great evolutionary story that led to "higher vertebrates" like mammals. In fact, more than half of all vertebrate........ Read more »
Buckley, J., Maunder, R., Foey, A., Pearce, J., Val, A., & Sloman, K. (2010) Biparental mucus feeding: a unique example of parental care in an Amazonian cichlid. Journal of Experimental Biology, 213(22), 3787-3795. DOI: 10.1242/jeb.042929
Khong, H., Kuah, M., Jaya-Ram, A., & Shu-Chien, A. (2009) Prolactin receptor mRNA is upregulated in discus fish (Symphysodon aequifasciata) skin during parental phase. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 153(1), 18-28. DOI: 10.1016/j.cbpb.2009.01.005
- November 7, 2010
- 06:30 AM
- 362 views
Just got vaccinated... again
by Daniel in Ego sum Daniel
I chose to get vaccinated for the seasonal flu this year as well! This is my post from last year. I think it's a good idea to get vaccinated, even if you're young and healthy. If nothing else, I'm making it a yearly statement in the face of the anti-vaccination loonies. Last year I got vaccinated for both the seasonal flu and the H1N1 or "swine" flu. Understandably last year's relative hysteria about swine flu is nowhere to be seen this year. But whatever happened after that? Wonder no more, the........ Read more »
Turner, S., Doherty, P., & Kelso, A. (2010) Q. BMC Biology, 8(1), 130. DOI: 10.1186/1741-7007-8-130
- October 21, 2010
- 02:03 PM
- 408 views
Einstein's brain
by Daniel in Ego sum Daniel
Einstein's brain was photographed only hours after his death. Ref: Falk (see reference below) Einstein's brain pops up quite often in popular science lore about the relation between brain size and intelligence. The most common myth (based solely on my own experience) is that Einstein's brain was smaller than average ergo brain size has nothing to do with intelligence. In actual fact, the size of Einstein's brain (as measured when retrieved shortly after his death at 76) was completely unremarkab........ Read more »
Spicer, K. (2010) An old brain with new tricks. Frontiers in Neuroscience. DOI: 10.3389/fnins.2010.00040
Falk, D. (2009) New information about Albert Einstein's Brain. Frontiers in Evolutionary Neuroscience. DOI: 10.3389/neuro.18.003.2009
- October 13, 2010
- 02:45 PM
- 343 views
Babies, balls and creationists
by Daniel in Ego sum Daniel
A recently published study in PNAS explores how small babies relate order and disorder, or entropy, to the different types of things that may cause them. Amazingly, babies as small as 12 months old show some understanding of the difference between the deliberate and goal-directed "agents" that can cause order, such as a person, and those randomly acting inanimate objects that cannot, such as a bouncing ball. This means that we have some sort of general understanding that the way agents act on t........ Read more »
Newman, G., Keil, F., Kuhlmeier, V., & Wynn, K. (2010) Early understandings of the link between agents and order. Proceedings of the National Academy of Sciences, 107(40), 17140-17145. DOI: 10.1073/pnas.0914056107
- March 11, 2010
- 05:34 AM
- 594 views
"Why do we believe", and are atheists really more intelligent?
by Daniel in Ego sum Daniel
ResearchBlogging.org editor Dave Munger has written an article for SEED magazine entitled "Why do we believe". The article summarizes recent blog entries regarding studies on the origins of religiosity. It's really worth reading to get a good overview of the subject, and what do you know he links my entry on god's will and beliefs in it.
Among the studies that are mentioned is a controversial study entitled "Why Liberals and Atheists Are More Intelligent" (link at the end of this post).
Medic........ Read more »
Kanazawa, S. (2010) Why Liberals and Atheists Are More Intelligent. Social Psychology Quarterly. DOI: 10.1177/0190272510361602
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