Friday, August 31, 2007
Anyone that knows me outside of the blogosphere, knows I won't turn down a good game of Mahjong. Hat tip to my dutch neighbours (everyones a blogger these days!) and mahjong score keepers (also maker-up of the mysterious special hands that give him 10,000+ yuan each freakin hand) for this strange article. According to Chang et al. 2007,
'Mah-jong epilepsy' is a rare reflex epilepsy syndrome, manifesting as recurrent epileptic seizures triggered by either playing or just watching mah-jong.And what was this epic study based on? (Trumpet sounds) A sample size of 3! Which we all know is the magic number. Each patient had no family history of epilepsy.
Case Study 1: 79 year old male, played mahjong for 8 hours, held a ready hand when onset of a generalised tonic-clonic seizure (GTCS) occurred. Upon admittance, normal neurological exam, EEG and CT. Man had a history of 2 other events while playing mahjong within the last 3 years. Stopped playing mahjong after 3rd seizure and has not had any since (8 years later).
Case Study 2: 42 year old male, seizure while playing mahjong. Normal neurological exam, EEG and CT as well. Abstained from mahjong, resumed playing mahjong after a few years. 3 years after resuming mahjong had 2 seizures while playing (even with resumption of medicine). Quit playing for good, seizure free for last 18 months.
Case Study 3: 39 year old male, seizure onset after 2 hours of playing mahjong. Unremarkable examinations and scans. Avoids mahjong now, no seizures.
The authors note that:
"Reflex seizures associated with mah-jong, brought on by either playing or watching the game, constitute a rare condition not recognised until recently. To date, only 20 cases of ‘mah-jong epilepsy’ (MJE) have been reported in the English literature."The mean age of onset was 54 years, range 34-76 yrs. (n=23), males outnumber females 10:1 and attack frequency ranged from one every 3 years to more than 30 a year (depending on x, y, z).
"Mah-jong is a cognitively demanding game. It involves substantial higher mental processing and outputs: memory, concentration, calculations, reasoning, strategies, sequential thinking and planning, consideration of alternative solutions, and a lot of decision-making. From this perspective, mahjong–induced seizures are best classified as a subtype or manifestation of cognition-induced epilepsy"Wait a second, thinking, calculating and making decisions can make you prone to seizures! Someone better tell my advisor this.
Actually its pretty interesting stuff. Understandably, its pretty rare and I am sure sleep deprivation after playing 10+ hours and stress over losing copious amounts of money contribute greatly. I can see how someone's cognitive system just shuts down or freaks out! Take it easy chinese people! Play with fake money instead and drink plenty of water!
Thursday, August 30, 2007
Below are my icon submissions for the BPR3 icon contest. Head over to Bloggers for Peer-Reviewed Research Reporting to support and join in the conversation! I like the magnifying glass because it not specific to a discipline, signifies taking a closer look at peer-reviewed research, and also signifies going into greater detail. The white background should go with any blog template.
120 x 90 entry
80 x 50 entry
16 x 16 entry
or a slightly more colorful image
The magnifying glass icon is absent for the 16 x 16 because I felt it just wasn't visible enough to be useful. I think it is more important to highlight BPR3, like the Sb in the address bar on the Scienceblogs homepage. Both icons are 4kb.
In the 80 x 50 entry, I put in only 'Report' because Blogger for Peer-Reviewed Research Reporting was too large to be effectively seen. It would have needed a smaller font. This icon though has the logo, the magnifying glass peering over BPR3, the web address and the the word 'Report' to signify it is a blog report on peer-reviewed research. This icon is 8kb while the largest one is 12 kb. So all these icons would take up little bandwidth.
Tuesday, August 28, 2007
Editor's note: This post was selected for publication in the anthology Open Lab 2007: The Best Science Writing on Blog.
The Anemone genome paper, that I previously had posted on, was a landmark paper in comparative phylogenomics. It provided a 'backbone' (yes, pun intended) for comparison from a supposedly more primitive state to a more derived state (i.e. arthropods, nematodes, mammals). The findings of the paper were very interesting, yet somehow they are being highly misinterpreted by certain factions, namely intelligent design "theorists". At the creationist blog, uncommon descent, there is blatant misinformation being spread about the findings. After reading the post and its comments, it is obvious that the poster and certainly the commenters have not bothered to read the paper. To really understand a scientific article one must move beyond the press releases and read the work as it stands.
As someone who has and currently is studying anemones, I would like to respond to some of the ID claims both from the original post and some of the more 'interesting' comments. I will proceed on a point by point basis:
1) The title: Where did sea anemones get human genes? The questions is inversely phrased. It should read Where did humans get anemone genes. Or more importantly, why did humans conserve genes from the last common ancestor between an anemone and a bilaterian.
Just how the heck is the Darwinian paradigm going to explain this? Advanced genetic programs installed before there was any chance of natural selection acting on them. Yikes! Another finding in the real world not predicted by, or even possible within, the Darwiniam paradigm. Another surprise for Darwinists.Yes, but for a different reason. Underlying assumptions are always tested in science. That is perhaps the
Sooner or later they’ve GOT to start questioning underlying assumptions. (Naive, ain’t I?)
With regard to "advanced genetic programs installed before there was any chance of natural selection acting on them", I'm not sure what you mean by advanced. The authors described the origins of eumetazoan genes, ancient genes (i.e. predating the anemone) comprise 80% of all eumetazoan genes. Natural selection did act on the other 20% of genes to give us the fantastic animal diversity that we see today, from the cnidaria to the chordata and everything in between (including the Lophophorata Christopher!). So most of the genetic programs were evolving over millions of year prior to the last common ancestor to the cnidaria and bilateria.
Inrons[sic] again. Funny how these sections of “junk DNA” keep turning up, conserved over hundred of millions of years, with no physical expression of them for natural selection to work on.The term 'junk DNA' is a historical term and a known misnomer to biologists. It is more readily defined as regions of the genome which no function has been identified as of yet. There are several reasons for its presence including that it is an evolutionary remnant from a time when one or several mutations rendered a coding region, insertions of transposable elements, or an unknown regulatory function. There conservation is a result of the lack of selection acting upon them. In fact in the quote above you are arguing for common descent. When genes get turned off that doesn't necessarily mean they go away. The net selective pressure purports greater exertion on physiology or morphology that is being acted on in the present, rather than reducing the genome size, which is not necessarily acted upon by external factors, i.e. no selection from the abiotic environment or biological interactions.
I need not add (but will anyway, for anyone who needs it spelled out) that Darwinism has NO explanation for where these complex genes came from. How can you have a program to build complex multicellular creatures before there are any such creatures for natural selection to work on? How can you select mutations and build gene programs before there is expression of the genes? Hmmmm?Evolutionary biologists do indeed have an explanation for the rise of complex genes, its called evolution, which coincidentally has been explaining biological phenomena for about 100 years prior to the advent of ID. The adaptations necessary to go from a single-celled organism to multicellular ones have occurred independently several times throughout evolutionary history. This is evidenced by statistically rigorous phylogenetic methods comparing single-celled protists with other multicellular eukaryotes. Hopefully someone can chime in with a reference for this. I have seen the data before but can't remember any studies and its late here... Additionally, mutations aren't selected for. An organism is not thinking that it needs a mutation so it can outrun its predator. Natural selection and indeed evolution, are reactive not proactive. We have seen evidence of rapid evolution in populations of species. For instance, snail shell thickening over 100 years with the introduction of an invasive crab is just one of many that come to mind. Snails with thicker shells survive more attacks by crabs and live longer to reproduce more often giving rise to progeny with the ability to synthesize thicker shells.
The following are some of the more intriguing comments:
"I’m still new here, but I can’t help but ask…do people actually read the articles before declaring they falsify evolution?"To which was replied in the next comment:
"I don’t think you fully get it. Those of us at UD (for the most part) have been following the NDEvo/creo and now NDEvo/ID debates for a long time. We are well versed in NDE and have long been making predictions of these sorts of things. Dembski and others have been doing the theoretical work which was dismissed by NDE proponents.Was the original commenters question answered? No, therefore I will answer the question to the best of my ability. No. It is clear that the people contributing to this forum did not indeed read the actual article. Else they might have been surprised themselves to learn about the genetic evidence for the common descent of all animal phyla from the eumetazoan ancestor.
So when we see stories such as this, they are just more emprical findings confirming predictions of ID. We see these sorts of stories all the time. Some of them, when contested, are read thoroughly and discussed in detail. Others are just “Ok, so Darwinism is surprised again, what else is new?”
Neo-Darwinism is already falsified (in myriad ways…stick around and pay attention); new findings are fun, because they show just how “onto something” ID really is."
2)OK there really isn't anything else worth my effort there, I'm just wasting my time.
Hat tip to Bug Girl for a great new resource: Tree of Life Podcasts! Perusing the list of awesome, yet highly educational, videos I came across this one about Arizona's very own species of trap-jaw ant, Odontomachus clarus. Trap-jaw ants are very interesting because they quite possibly are the record holders for the fastest movement in the animal kingdom! O. clarus is even more remarkable for being able to pull back its mandible 180 degrees. The movie itself is worth watching for the defensive bouncer and escape jumps. Enjoy!
Monday, August 27, 2007
Wifey has a great picture on her blog with elliot "enjoying" the water. I believe his words were, and I quote, "Oh no! Oh no! Oh noooooo!" On the last day he finally allowed water to touch his feet though and even seemed to enjoy it.
Courtesy of McClain and Etnoyer at Deep Sea News, I have been bestowed the enviable Thinking Blogger
"all that is invertebrate and just plain great, informative writing"I was actually bestowed the title of a Thinking Blogger a month ago. Thanks guys! I wouldn't have gotten my blog start if it wasn't for my short but sweet tenure as a guest blogger at DSN between March and May with the From the Desk of Zelnio column. I am supposed to bestow this
1. David Colquhoun at DC's Goodscience. He is a Professor of Pharmacology at University College London who exposes the "idiocy of metrics" in measuring science and scientists and discusses the adverse effects of the "cult of managerialism" at universities and in science itself. As a young aspiring professional, I have learned a bit about the industry here. Though only 2 months old, I hope he will continue enlightening us with his extensive experience in the university world.
2. Aydin Örstan at Snail's Tales, whose blog has continued to educate and intrigue me about the world of gastropodous mollusks.
3. Emmett Duffy at The Natural Patriot, mostly because I was a fan of his research before I knew he had a blog. His blog highlights the reasons why science, conservation and environmentalism are patriotic concepts. He brings up relevant issues and has the bigger picture in mind. Emmett, you are THE natural patriot.
4. Christopher Taylor at the Catalogue of Organisms, a fellow taxonomically-inclined blogger, for his exceptionally detailed posts on all things organismal. Once you read one of his posts, you can tell he has put alot of time, effort and research into each well-crafted article. Keep up the good work Christopher and don't believe a word he says about the Lophophorata...
5. The "degenerate grad students" (all 8 of them) at Bayblab and not just for playing my songs on their alcohol-influenced science podcasts. These crazy Canadians write entertainingly on all areas of science, though mostly molecular, cell, genetics oriented material. Plus a monthly podcast talking about some of their most interesting posts! If you haven't bookmarked Bayblab yet, you are making a grave mistake!
Saturday, August 25, 2007
This weeks Spineless Song is a collaboration with Christopher Taylor from the Catalogue of Organisms. He wrote all of the words (though I tweaked 1 or 2 here and there) and I did the music. As always, the song is in the sidebar.
Brachiopods (arm-foot) are not only weird, they are freakin' weird. They are members of the clade Lophophorata (fun to say!) meaning they possess a special organ called a lophophore. This odd organ fuctions in feeding and the structure is shared with ectoprocts (a.k.a. bryozoans, the mossimals) and phoronids (Mr. Byrnes do you still have My Phoronid online??).
Ballad of the Inarticulate Brachiopod
I am an inarticulate Brachiopod form
Just an ordinary linguloid trying to keep to the norm
I keep my bauplan unchanged hundreds, millions of years
While articulates diverge madly, I prefer a lower gear
Phosphatocopids, Hyolithelminthes no longer here with me,
And yet I still wear phosphate no carbonate you see
Those aragonitic taxa with their diversity of forms,
May think themselves above me, may think they've won the war.
But I'll bet you dimes to horseshoes that when they've had their run
I'll still be here just simply unaltered in the mud.
Posted by Kevin Zelnio at 11:26 PM
"Right now, 30 percent of all hermit crabs on our shorelines are living in shells that are too small for them. In the springtime, when the animal has its growth spurt, this shortage skyrockets to 60 percent. Hermit crabs, whose own bodies provide only thin exoskeletons, must scavenge and appropriate hard-walled shells abandoned by marine gastropods for shelter. The problem is that there currently are not enough shells left on our beaches for hermit crabs to use. This situation is not only uncomfortable but dire."-Demaray 2004This is the warning from an article by Elizabeth Demaray 3 years ago in Cabinet Magazine. This still rings true today. S.A.L.-P. and I have done our part by adopting 3 unfortunate hermit crabs from a misorder by our intro bio labs, but we are only 2 graduate students. This issue is bigger than us.
Thank Hey-Zeus that there are architects working day and night on this important issue facing the world's hermit crab population. Based on a design from 1930's fascist Italian architect Giuseppe Terragni, the Hands Up Project has produced a plastic hermit crab shelter that will revolutionize the hermit crab housing industry. It is lightweight, comes in various sizes and colors, high internal volume and contains a post for the crab to hold onto with its claw. The Lexus of hermit crab homes if you ask me. Hermit crabs everywhere are breathing a sigh of relief knowing that there struggle in finding a home is significantly lessened.
"As might be imagined, even without the current housing shortage, the finding and exchanging of shells is a preoccupation amongst this species.[...] Based on what we know about the new needs of these animals in their current environment, the Hand Up Project proposes to manufacture alternative forms of housing, specifically designed for use by land hermit crabs, out of plastic. This solution offers multiple benefits. Not only will the project afford the animal badly needed additional forms of shelter, but we also contend that, by utilizing current technology, we may now be better equipped to meet the needs of this life-form than nature ever has."Demaray 2004
Please do your part today. If you cannot adopt and provide a home for a hermit crab, buy or make shelters for them and
*Last two photos from the Demaray article.
Well I am back from the beach in Delaware. It was a nice time though I much prefer tidepools and rocky shores to explore. This was my first time to Delaware and to a east coast beach (in my memory anyways). While South Bethany Beach was great, I was amazed at how built up the area was. Lot of condos and houses, no shortages of tourist shoppes and restaurants. I am no stranger to urban sprawl of course, but it seems out east here they build upon any possible substrate available. If its not available they fill in a marsh to make it available! I really to go back though when the kids are older and do more outdoors activities. We passed by lots of great marsh that I'm just betting is hiding all sorts of great finds. I'll have to pack a kayak and my dry bag next time. It was nice to have some warm ocean water though! Can't barely wade in California's water without going numb.
Though the ride down was probably one of the most stressful times of our lives, my wife had the brilliant idea of driving back at night while the kids are sleeping. Lets say we shaved off about 4 hours (compared to driving down during the day)! There is lots to catch up on! Some great articles in the last week or two and of course a new Spineless Song. Since I didn't have internet access this week and missed the Tuesday Toon, I leave it here below!
Bonus song lyrics, found by my officemate/labmate/neighbour S.A.L.-P. (interesting arrangement of initials... props go to the first person to recognize what phylum the initials belong to...).
from Ronald Shimek's A Spineless Column at Reefkeeping
Don't you ever laugh as a hearse goes by,
For you may be the next to die.
They wrap you up in a big white sheet,
And cover you up from your head down to your feet.
They put you in a big black box,
And cover you up with dirt and rocks.
All goes well for about a week,
And then your coffin begins to leak.
The worms crawl in, the worms crawl out,
The worms play pinochle on your snout.
They eat your eyes, they eat your nose,
They eat the jelly between your toes.
A big green worm with rolling eyes,
Crawls in your stomach and out your eyes.
Your stomach turns a slimy green,
And pus pours out like whipping cream.
You spread it out on a slice of bread,
And that's what you eat when you are dead.
Tuesday, August 21, 2007
You may have noticed a bit of inactivity on my blog, which is highly unusual given my tendency to blabber. That is because I'm with my family in South Bethany Beach for the week for a little vacation. This is my first time to an east coast beach. We are enjoying it, the water is warm and delightful. South Bethany is significantly less crowded than other nearby beaches too. This is my son's first time to the beach (aside from being a small baby on the baltic coast of Sweden). The first day he was very hesitant, clearly scared of water coming toward, though fascinated and in awe of the ocean. By afternoon he was playing with his truck in a puddle created by a few rogue waves earlier.
Today he was doing great in the morning. We walk a ways up the beach he poked his finger in crab burrows and said "hole", picked up shells and promptly tossed them, chased a tern around saying "bye bird" and trampled over the remains of yesterday's sand forts. But in the afternoon, after his nap, he wanted nothin to do with puddles and enticingly warm water, or wet sand for that matter. He did everything possible to avoid getting his feet in the water. So instead, we went to the boardwalk at Rehoboth Beach and walked around where he was absolutely goggle-eyed at the sights and sounds of all the arcades we passed.
I naively brought a collection kit consisting of 95% ethanol, nalgene jars, label tape and a sharpie. Of course my brother gave me the Geek of the Week award for bringing a collection kit on my family vacation. But hey when opportunity arises, I'd like to be prepared! I need to collect zoanthids for a phylogenetic project being start up by myself and several colleagues. The naive part is that I wasn't aware Delaware was nothing but sand. Not a rock in sight, nothing for clinging critters. BORING! The invertebrate life is pretty sparse here. I've seen a small crab, some kind of strange burrowing "shrimp" (looks like a shrimp but with a highly reduced abdomen folded tightly underneath so as to appear like its only half an organism!) and a copepod that burrows in the sand. The beach is very nice though. If anyone knows where I might be able to collect zoanthids in Southern Delaware or Northern Maryland or any type of rocky intertidal type habitat in the area, please let me know ASAP. Can you tell yet that I am used to the coast of CA? So much great stuff to go tide-pooling over there!
Saturday, August 18, 2007
But my confirmation period occurred concomitently with my rebellious period. Rebellious to me meant reading alot of philosophy, both the well-established classics and the modern beat, punk and hip-hop of the late eighties and early nineties. The more I got into reading, the more I began thinking, which we all know is a dangerous thing. I started getting very much into the history of religion. This turned me off even more as I learned of the systematic abuses of religion towards non-believers of a particular faith but also to a particular faith's own followers. In my midwestern idealistic sheltered world, I learned that Jesus' teachings were of love and equality, that Moses wrote down God's word as 10 commandments and the lessons of the various books highlighting how to live good decent lives and practicing random acts of kindness in God's name. The reality that exploded before my impressionable teenage eyes was far more brutal and gruesome. It was one of pure and utter hypocrisy, manipulation, greed, and severe brutality.
I understand that the majority of religious believers are great people who practice their faith in earnest and pay heed to good teachings of selected passages in the Bible. But reality depicts a organization profiting off the welfare of its congregation in absurd ways. This is far beyond the "problem of evil". This relates to a very human condition - power, authority, control. It is because practice doesn't align itself with preach that I cannot believe in God. An atheist knows there is not a God, as opposed to an agnostic who feels it cannot be proven either way. I know there is no God by the actions of those who purpose to be the bearers of God's words. It is a very painful thing to know too. I want to cry when I talk about it. Deep in my heart it would feel so good to believe. The practice of religion and religious ritual can be a very joyous experience. I feel inspired watching the devotion and hearing the choirs practicing at night when I was in Fiji, a country very devoted to practicing the good in the "good word". The mere idea of an afterlife is beautiful, if false. To be reunited with loved ones in the Kingdom of Heaven would be a experience... to die for. But reason cannot allow me to have faith. Mark Twain once said "Faith is believing what you know ain't so."
This is all to say not only that I'm an Atheist, but proud to be one. I am proud that I can see the smoke and mirrors, the games, the lies, and see the atrocities for what they are. I am proud that I have taught myself the ability to reason out social and philosophical problems without throwing up my hands in the air and mentally giving up saying that its God's will. I am proud that I came to this decision on my own accord, though originally out of rebellion to authority from an awkward time in my life, I did my research and genuinely wanted to believe. It hurt my parents and grandparents when they learned I became an Atheist. These are the people I loved most in my life and I was confused that I could see through their religion and they couldn't. I am proud to know and love science, which has taught me that because we know not an explanation for something today does not mean we will never know it. This is why I support the Out Campaign and will proudly display the Scarlett A on this blog.
Friday, August 17, 2007
Got them deep Bdelloid Blues? You know the ones I'm talking about. When a woman don't no man. When times get so bad you just gotta dehydrate and wait out the storm. This song was inspired by, and lyrics co-written with, Aydin Örstan of Snail's Tales. Liquid inspiration provided by Kevin Z's homemade Aquavit. As you might tell from this odd recording (i.e. slurred words, fuzzy overlaid solos) I was fairly well inspired...
I don’t need no male
I don’t need no sperm
I don’t need no hemmorhoid
Cause I’m just a parthenogenic bdelloid
You took my resources
You took my water
I ain’t annoyed
Cause I’m just a parthenogenic bdelloid
is what I got
When times get bad
I don’t rot
Just hide and seek
Waitin for a little rain
I don’t need no Lloyd
Cause I’m just a
biological species concept hatin
Update: I don't know why I added trochophore, can I blame it on the booze? Rotifers do not have trochophore larvae. Although noted in Jenner 2004:
Nielsen (1987, 1995, 2001) advocates the homology of the rotiferan trochus with the prototroch and the cingulum with the metatroch of trochophore larvae, an argument followed by Peterson & Eernisse (2001).[...] Although these homology proposals are not buttressed by cell lineage data on the source of the ciliary bands in rotifers, they are in accordance with the widespread view that rotifers are paedomorphic animals with respect to taxa that possess trochophore larvae[...]. available comprehensive morphological or total evidence (+ 18S rDNA sequence data) cladistic analyses frequently position Rotifera outside a clade Trochozoa (characterized by trochophore larvae)[...]. The paedomorphic origin of Rotifera and homology of their ciliary bands with those of trochophore larvae thus remain dependent upon out-group comparison and the assumption of a trochus and cingulum in the rotiferan ground pattern.
Hot off the press releases, The Dauphin Island Sea Lab in Alabama is reporting the presence of the jelly Phyllorhiza punctata in Gulf of Mexico waters.
"first reported in great quantities in the Gulf of Mexico in 2000, has made a vigorous reappearance this summer in waters from southwestern Louisiana to Morehead City, North Carolina."-ScienceDailyPhyllorhiza punctata is originally from Australia and is hypothesized to have came through the Panama Canal about 50 years ago. Though the medusa stage is the nuisance (fouls trawl nets and consumes eggs and larvae of commercially important fish), it is the polyp stage that needs to be targeted for removal. A single polyp can bud off dozens of jellies in a single event and live for a long time, thus resulting in potentially hundreds of medusae over its lifetime. Yet, virtually nothing is known about the polyp stage of Phyllorhiza punctata because of its small size and unknown habitat. They are also very prolific comsumers. Dauphin Island Sea Lab Senior Marine Scientist Dr. Monty Graham states that,
"...they can compete with commercially important fish for food, and they also eat the larvae of these fish. In their native waters, they tend to be fist-sized; here in the Gulf, they can be a big as dinner plates."-ScienceDailyThe Dauphin Island Sea Lab is asking for your help. If you live in coastal Gulf of Mexico or Mid-Atlantic states and sight this jelly, you can report it at a website called DockWatch and follow these instructions to aid them in understanding of this invasion.
"What can people do now? The most important response is to provide scientists with information when Phyllorhiza is observed. This DockWatch web site is just one way to let us know when and where you saw a jellyfish[sic] (not just Phyllorhiza, but all jellyfish[sic]). People can also call us at the Dauphin Island Sea Lab using a direct line to a recorded message (251-861-2289). Also, Dauphin Island Sea Lab scientists need tissue samples of Phyllorhiza. Since the jellyfish[sic] does not have a painful sting, it is easy to collect the jellyfish[sic] into a large zip-lock baggie and freeze it until it can be picked up by one of our scientists. If the whole animal cannot fit into a baggie, then taking a slice of the animal will suffice. Be sure to freeze it right away and call or submit your information using the web site."-DockWatch
Thursday, August 16, 2007
Wednesday, August 15, 2007
There is a growing movement among many science bloggers for an icon that says a particular post offers thoughtful comments and analysis on an article from the peer-reviewed literature. The Mungers from Cognitive Daily have posted on this topic here, here and here. There has been great participation and great ideas thrown around in the comment threads! I suggested the name BPR3 for Bloggers for Peer-Reviewed Research Reporting, which seemed to go over well. The icon has much more meaning though. Many of us hope that it will serve as a gateway to an aggregation feed for reporting by bloggers on peer-reviewed research. Whenever someone posts the icon on the blog post, it can link back to feed-blog. Conversely, you can use the main feeder blog to find interesting analysis by bloggers on peer-reviewed research.
BPR3.org was just launched today and will serve as main discussion website. I encourage every blogger who reports on peer-reviewed research in one or another to get proactive on this initiative early and share you voice on how to make this a worthy, user-friendly, and useful idea. I personally think its a great idea that gives bloggers more credibility, highlights literature that may typically doesn't make it to the press releases but has some significance in a field, and provides readers and authors of peer-reviewed research a centralized gateway to find interesting articles and hear different perspectives on that research. This could potentially be of enormous interest to the authors of the papers in order to gage the impact of and interest in their article or find any errors or other interpretations, as the blogosphere can be very critical of what is out there in the public domain. Journals should also be interested as well to measure the interest in their articles that is generated outside of citations. I can think of many examples where the research was very interesting and important to a certain field but gets cited very little, usually due to the size of the field.
So designs are being sought out for the icon. Below is my entry. I welcome any suggestions in the comment thread here of at BPR3.org.
What it looks like smaller, the size it might most commonly be used at:
http://www.blogger.com/img/gl.link.gifToday I downloaded my 3000th reference to my Endnote library! What a milestone. What was the lucky paper? It was none that John Wilkins', from the blog Evolving Thoughts, Festschrift to Ernst Mayr published in Biology and Philosophy here. Congrats on the pub John, looking forward very much to your Species Reader. Send a copy my way and I'll do a thorough review of it!
Tuesday, August 14, 2007
Bayblab podcast Episode 11 part 2 is available on their website (or for download on iTunes if you subscribe to their podcast).
"On this segment we talk about unusual animal penises, drug policies in Canada and we introduce the food challenge! With musical guest Kevin Z."Penises, drugs, food and my music! What more could you ask for?
And if you are under 13, I'm going to have to ask that you leave or get your parents to email me their permission that you can view it.
I earned the 13 and above rating for the words Hell, Dead and Porn. I think Mr. Taylor at the Catalogue could take a few lessons from me (talk more about invert-o-porn man!!). After this post, I am sure my blog rating will go to R for mentioning penises and drugs.
Posted by Kevin Zelnio at 7:36 AM
Monday, August 13, 2007
Here are some great posts from the blogosphere that I don't have time to do posts on myself.
First, Christopher Taylor at the Catalogue of Organisms beat me to it. He did a great job reviewing the recent PLoS ONE paper revealing how Acoels are not flatworms. In my ongoing efforts to battle paraphyletic nomenclature, Acoels shall not longer be called flatworms or "acoel flatworms". Find out where they fit at the Catalogue for an in-depth analysis of the paper.
Second, the LiveScience blog posts on new research published in Pain 'N the ASs on the evolution of body size in beetles. While palaeo-beetles were huge, modern-day beetles are pretty small by comparison. This study reports that
"bigger beetle species devote a larger portion of their bodies, proportionately, to airways than do smaller species. And the air passageways that lead from the body core to the legs turn out to be bottlenecks that limit how much oxygen can be delivered to the extremities."-Alex Kaiser, study lead author
Third, awesome song, awesome song lyrics
"There's nothing so pure as the kindness of an atheistIt's a beautiful song that is worth the $0.99 on iTunes (where you preview 30sec. of the song too). I found the chords for it and will cover it this week and add it to my list of insurgent country music.
simple act of unselfishness that never has to be repaid
And there's nothing so sure as a razor blade above your wrist
When you think you just can't stand it
That you're gonna leave empty handed
Do you still dream of being saved"-Freakwater's Gone to Stay from their Old Paint album
An intriguing new study by Bachar et al., published in the latest Journal of Experimental Marine Biology and Ecology (JEMBE) shows that carbon derived from different metabolic pathways is used differently by anemones with algal symbionts. It has been well-known for a long time that some anemones, such as the Aiptasia sp. used in their study, form a symbiotic relationship with zooxanthellae (called autotrophy). For a while it was assumed that the anemones persisted by mostly utilizing carbon translocated from its symbionts, but they can also supplement this by heterotrophic feeding on plankton. Bachar and colleagues studied the fate of carbon derived from autotrophy versus the fate of carbon derived from heterotrophy using radiolabeled carbon sources.
To trace the fate of autotrophic carbon the standard is to radiolabel carbon dioxide (14C via sodium carbonate) since this is the carbon substrate of photosynthesis. To trace the fate of heterotrophic carbon they grew brine shrimp (Artemia sp.) fed on algae incubated with the same radiolabeled carbon dioxide source. This what is called a pulse-chase experiment in symbiosis lingo. The idea is that you pulse the anemone with labeled seawater for a certain amount of time, for instance 12 hours in the light and 12 in dark in this study. Then, there is a chase period where you take the anemone out of its radiolabeled environment and let it "digest" the carbon. It is during this time that the products of photosynthesis are making its way from the zooxanthellae into the tissues of the anemone. Then you make an anemone slushy, basically using something resembling a modified coffee bean grinder. Centrifuge the sample, all the algae fall to the bottom while the animal cells lyse into the supernatant. Add a dash of acid to drive out unassimilated inorganic carbon and Voila! You have yourself a delicious Anemone Slushy, a tasty family treat.
What Bachar et al. did was to trace the fate of carbon in the lipid portion of the Anemone Slushy as well as the whole tissue (i.e. animal) portion of the slushy. What they found was very interesting.
"The radioactivity levels of both the lipids and the total tissue of the sea anemones that were fed labelled autotrophic or heterotrophic carbon show that for the autotrophic anemones, the fastest change occurred in the lipid tissue, while for the heterotrophic anemones, it took place in the entire tissue."-Bachar et al. 2007 (see Fig. 2 from their paper below)
This is the first I have seen (and they make that claim in their abstract) that differentiates between the fate of autotrophically and heterotrophically derived carbon in a mixotrophic organism. It suggests that autotrophically derived carbon is convert mostly to lipids, potentially as quick and dirty carbon source for metabolism and respiration, while heterotrophically derived carbon is dispersed throughout the body, possibly for structural purposes (i.e. cell membranes, growth). Autotrophic carbon, derived from carbon dioxide, is short chain molecule so it makes sense that this would be used as an immediate energetic source since it can be easily converted into molecules like pyruvate and acetate which can slide right into the the metabolic cycles. On other hand, heterotrophic carbon is typically longer chain, like fatty acids and sugars, which need to be broken down into smaller parts to be used for metabolism. Hence these might be more appropriate carbon sources for structural components which are typically longer-chain carbon compounds like collagen and phospholipids.
Though this a short study reporting their novel results I am sure they have much greater ambitions in the works so it is worth keeping an eye out for future work from this lab. Symbiosis is fascinating topic. Though scientists have known about algal-cnidarian symbioses for a long time, it has taken decades of work to just figure out what and how. Now Bachar et al. give us where and some further insight in some more how. It is still unclear "why" though and the "how" in an evolutionary sense. Symbiosis is a field still much ripe for exploration. All the studies ever done on host-symbiont phylogenies, carbon translocation, physiological ecology, etc. is just the tip of the iceberg. Autotrophic symbioses are everywhere and occur in many animal phyla from cnidarians to nematodes to molluscs. Some ugly hairy creatures with backbones (a lame evolutionary feature is ask me) of the overexaggerated 5% even form symbiotic relationships with autotrophic organisms!
Hat tip to Bayblab for this great quote, posted on the Department of Biological Science at Lehigh University website as a disclaimer (where Michael Behe still pretends to be a biologist):
"While we respect Prof. Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally and should not be regarded as scientific." (emphasis mine)Oh Snap! In your face biznitch! Invertebrates everywhere are raising claws, tentacles, and antennae in support of the Dept. of Biological Sciences at Lehigh.
Saturday, August 11, 2007
Cool stuff! Bora from A Blog Around the Clock has posted an interesting piece giving evidence for biological clocks in the phylum Porifera, sponges if you will. It definitely worth a good reading. For instance, did you know that sponges can move!
"the whole animal rearranges itself as cells move over each other, pulling the spikules along."-Dr. Bora
Friday, August 10, 2007
The 151st edition of the Friday Ark is now online for boarding over at the Modulator. In addition to my own contribution on pimped out jumping spiders, the invertebrates are represented by a Leafcutter Bee, Widow Skimmer, Wasps, Catepillars, Bivalves on toast, Squid, Dragonflies, and a Moth.
The latest innovation from DARPA's Office of Creepy Technologies comes from Dr. Amit Lal, who wants to use controllable flying insects for surveillance missions. So far, his teams of engineers have managed to implant electrodes into moths during the pupa stage of early development, with minimal tissue damage. Video monitors show the insects as fully grown adults that can be induced to flap their wings in any direction. They're also working on a way to use the moth's living body—its movements and metabolism—as a power source for the implant's electronics.
DARPA's government-financed mad-science programs originate with managers like Dr. Lal.-Slate.com
Hat tip to my brother Ryan Z for this article from Slate.com titled I Want to Become a Mad Scientist.
Thursday, August 9, 2007
Inspired by recent research by Johnson & Yund that I posted on here, I transformed a classic Cyndi Lauper song into a Urochordata masterpiece. Well, thats for you to decide. If you don't know the song this is sung to, step out of the cave... Liquid courage brought to you this week by Dale's Pale Ale from the Oskar Blues Brewing Company.
Sea Squirts Just Want To Have Fun
I’m attached to rock in the moonlight
My colony says 'when you gonna live your life right?'
Oh but females aren’t the fortunate ones
And sea squirts, they want to have fun
Oh sea squirts just want to have fun
One sperm come in the middle of the night
My colony yells 'what you gonna do with your life?'
Oh ascidians, I can’t have only one,
But sea squirts, they want to have fun,
Oh sea squirts just want to have
That's all they really want...
When the filter-feeding day is done
Oh sea squirts they want to have fun
Oh sea squirts just want to have fun
Many males enter my siphonal canal
I don’t care how many, I’ve got eggs for them all
Some may say I’m too promiscuous
But sea squirts just want to have fun
Oh sea squirts just want to have
Not only do jumping spiders "drop it like its hot" to impress the hotties on the dance floor. Asian jumping spiders, not to be outdone by counterparts elsewhere in the world, flash a little bling bling to catch the ladies' eye. Taylor & McGraw report in the latest Current biology, that three-layered "scale sandwiches" of chitin and air produce a brilliant iridescent display that simply irresistible (photo to left, from Taylor & McGraw).
Only the scales of males reflect UV-light which the females can see, though humans being so intelligently designed cannot. When viewing a mirror image of themselves,
"males displayed aggressively to their mirror image, as we would expect one to behave towards a rival male; however, when UV light was filtered out, the males behaved differently, often courting themselves."-Taylor & McGraw 2007They are so sexy even they can't keep their chelipeds off themselves!
"Females also seem to be paying attention to UV coloration in males; in experiments where UV light was filtered out, females ignored male courtship displays."-Taylor & McGraw 2007Chica-chica bomp bomp oh yeah. Bang a gong and get it on.
Apparently, some really nerdy humans studied their scales and found that
"...each scale is composed of a sandwich structure with two outer corrugated chitin plates surrounding a thin layer of air (Figure 1C). This structure functions as a multilayer reflector, whereby the alternating layers of chitin, with a high refractive index, and air, with a low refractive index, organized at just the right periodicity with respect to the wavelength of light reflected, result in constructive interference, as light reflected off each interface emerges in phase"-Taylor & McGraw 2007yadda yadda yadda. Whatever. This is just nerdspeak for male jumping spiders are the sexiest invertebrate in the Kingdom. Jumping spiders are so hot, just looking at the image above makes my retina sizzle.
There is always a mollusc involved it seems. The July 13 issue of Science reports on major research titled "Magmatic Gas Composition Reveals the Source Depth of Slug-Driven Strombolian Explosive Activity"
Clearly, there is no reason to actually read this paper, it is clear from the title the slugs are driving highly explosive volcanic processes from deep with the Earth! Quite amazing really. From This Week in Science,
"The explosions are thought to be caused by gas slugs that rise faster than the surrounding magma and generate seismic activity near the surface of the volcano.[...]. they show that gas slugs form 3 kilometers beneath the summit craters, at the base of the volcanic pile and away from seismological processes at the surface."
Wednesday, August 8, 2007
I found some a great quote and analogy from an essay in the most current Current Biology by Peter Lawrence titled The mismeasurement of science. This essay takes a look at how science is measured and examines the use of impact factors and other metrics used to measure scientific progress for individuals, departments and institutions.
The quote is actually from Leo Szilard, the famous Manhattan project physicist. When asked by a wealthy entrepreneur who believes that science has progressed too quickly, what should be done to retard this progress, Szilard replied:
"You could set up a foundation with an annual endowment of thirty million dollars. Research workers in need of funds could apply for grants, if they could make a convincing case. Have ten committees, each composed of twelve scientists, appointed to pass on these applications. Take the most active scientists out of the laboratory and make them members of these committees. …First of all, the best scientists would be removed from their laboratories and kept busy on committees passing on applications for funds. Secondly the scientific workers in need of funds would concentrate on problems which were considered promising and were pretty certain to lead to publishable results. …By going after the obvious, pretty soon science would dry out. Science would become something like a parlor game. …There would be fashions. Those who followed the fashions would get grants. Those who wouldn't would not."
The analogy is Lawrence's own and relates to song writers being assessed in the same way as scientists, an analogy I can understand having came to science from the music industry.
"It is fun to imagine song writers being assessed in the way that scientists are today. Bureaucrats employed by DAFTA (Ditty, Aria, Fugue and Toccata Assessment) would count the number of songs produced and rank them by which radio stations they were played on during the first two weeks after release. The song writers would soon find that producing junky Christmas tunes and cosying up to DJs from top radio stations advanced their careers more than composing proper music. It is not so funny that, in the real world of science, dodgy evaluation criteria such as impact factors and citations are dominating minds, distorting behaviour and determining careers."
A Scientific "Audit Society"
Lawrence suggests that our scientific "audit society" has put meeting the demands of the holy impact factor above understanding nature and disease. He predicts that citation-fishing and citation-bartering will increase. Citation-fishing is putting your name on authors lists when you basically did nothing, like provide a reagent. I am not entirely sure what citation-bartering means, but I suspect it has to do with journals "encouraging" submitters to cite more articles out that journal to facilitate acceptance of the paper.
One problem I have thought about using standardized metrics to evaluate scientific progress is the aggregation of high citation potential research in only a handful o the "top" journals. Instead of a more even spread of the literature in journals appropriate for certain paper, the trendy research of the day is published in high profile journal, while the more topical journals are left in the dirt. This prevents lower "impact" journals from escaping a certain impact factor range, making them less appealing to new researchers whose papers fit more in the journals interests and could have been potential read by more people in their field. Getting your paper read by the right people is the real impact in my opinion. I recently submitted a species description to a journal in which several descriptions of species in the in family have been published, in hopes it would reach the broadest audience. My next paper I hope to be open access though.
"Impact" and Taxonomy
Standardize metrics, namely the impact factor, have a tremendously negative impact on taxonomy and taxonomists. This has in part to do with the behavior of most scientists with regards to the field. Taxonomic works are virtually never cited in references of papers. In ecology this is the most pervasive because ecologists often use detailed keys and species descriptions in their work to confirm the identifications. The species is the fundamental unit of biology, especially in ecology. Yet you never see statements in the materials and methods section of such papers that "polychaetes were identified to genus using Fauchald 1977". Meigen 1830, which described Drosophila melanogaster, should be the most cited publication that ever existed, based on the amount research published using that species.
Ecologists often ID specimens on hearsay. By this, I mean someone told them what this species was so therefore that is what it will be called. This is how I started out. Senior grad students had done most of the identifying work for me, I just needed remember the species list or compare what I find with what was on the shelfs. The problem with this was either the preliminary IDs were sometimes wrong or or closer examination resulted in one species being 2 or more. The former has resulted in the shrimp description now in review and the latter resulted in an several anemone descriptions still in progress. I can't underscore the importance of checking the facts for yourself!
The profile of taxonomy will greatly benefit if people include citations to the works they used, whether individual species descriptions, large monographs, revisions or identification keys. Taxonomic works are consistently the only publications that get more used and more systematically ignored by the "big science" community, including medicinhttp://www.blogger.com/img/gl.link.gife, molecular biology & biochemistry, and evolutionary biology in addition to ecology. This attitude towards taxonomy, and the managerial approach to modern science practices, has devaluated the stature of the taxonomist to providing a service, essentially for free, for the greater community without due recognition. This is exploitation. While jobs become scarce, funding even scarcer, demand increases because of the top heavy age structure of taxonomists. This is especially true in the U.S. where most biology majors will never see a systematics class in their undergraduate handbook.
I would also like to highlight a blog, called DC's Goodscience run by David Colquhoun at University College London, that I recently discovered that
"...exposes the idiocy of ‘metrics’ for the assessment of research quality by means of actual real-life examples. The aim of the blog is to provide a forum for discussion of the effects of the cult of managerialism on universities in general, and on science in particular."
Update: Christopher Taylor at the Catalogue of Organisms gives a perspective on the importance of taxonomy using an example from Harvestman (Opiliones, an arachnid).
Tuesday, August 7, 2007
Carl Zimmer from The Loom is asking scientists to reveal their science ink. Though I got these before I was ever interested in pursuing science as a career, I certainly think these fit in.
I plan to get a shrimp species I described tatooed once the description is published.
This week's Invert-a-toon is from The Department of Environment and Water Resources of the Australian Government publication "An overview of the conservation of Non-marine Invertebrates in Australia" by Alan Yen and Rhonda Butcher.
Monday, August 6, 2007
Every Friday I've been posting a new Spineless Song for you the public to enjoy. I have no problem songwriting after a few rounds of my homemade Aquavit or my current beer of choice, Old Chub and Dale's Pale Ale from Oskar Blues Brewing Co. in Colorado. But I am now taking requests for this week's and upcoming Spineless Songs. So use the Post Comments Feature and request a song about your favorite invertebrate, feel free to suggest context, plot, lyric lines, etc. Anything goes so long as it Spineless. I am currently working on Sea Squirts Just Wanna Have Fun, related to my sea squirt post a week and a half back. Though parodies are great fun its time for a complete original.
Head over to Bayblab to listen to their monthly podcast highlighting and analyzing all the science of the past month from their blog, including the science of beer. This month they end their podcast with my song, Big Dead Squid.
Go to Bayblab podcast Episode 11 - part 1 of 2 and take a listen
Sunday, August 5, 2007
Just a quickie, no pun intended, to guide readers over to Zooillogix for an awesome video of a jumping spider mating dance. Make your volume is on, the sounds are unreal! Click here for some bootyliscious jumping spider foreplay.
Invertebrates are not only the most diverse and interesting group of organisms to ever exist, they are also quite tasty! I very much enjoy a good crawdad, some crab cakes, or shrimp cooked in various ways. Once a week we have a pizza night. I often make shrimp and veggie pizza. Here is my recipe for this crustaceous creation!
Here is what you'll need:
1. Ready made pizza crust
2. Pizza sauce, I use Garden variety from Nature's Promise
3. Cheese, shredded. I usually mix several different types depending on what I have on hand
4. Shrimp, I use sustainably harvested arctic shrimp from Canada. They actually taste much better than the larger species from Indonesia. (see Shifting Baselines for a shrimp discussion).
5. Veggies! And lots of them! For this pie I used Zucchini, Avocado, fresh Dill, Chives, Corn and Green Pepper
Put it all together, bake at 400F until brown and crispy and Voila! A delicious shrimp pizza!
Just look at the way that gorgeous crustacean is all nestled in with the avocado, a sprig of dill and luscious melted cheese (a blend of jack, cheddar, parmesan, romano and havarti... just because I can). The red of the tomato sauce really provides a stunning background for what later become a delicious meal.
Now nothing goes down better with Shrimp Pizza than Kevin Z's homemade Aquavit! Its a very simple recipe from a brilliant norwegian cookbook I own called Kitchen of Light. It is a fascinating book, providing great recipes, beautiful photos of Scandinavia, stories and background on several of the meals.
For this you will need:
1. 725mL Vodka, Absolut of course!
2. Lemon, Lime and Orange peel. I use the full peel of lime and orange, but only half the peel of the lemon as my first batch, the lemon was overpowering
3. 1 tablespoon each of Fennel seed and Caraway Seed
I mixed all the ingredients in a separate container, but you can let them marinate in the vodka jar if there is enough room. A couple shots ought to clear out enough space for the ingredients! I let it marinate for 3-4 days in a sunny spot.
The golden color is nice. After it is done marinating, next comes the filtering. I reused some nice bottles a dutch friend and I emptied out over the course of a few months. Oh yummy Beerenburger... why did it have to end!
I filtered the liquid using a funnel and coffee filter. You'll have to remove the rinds periodically. I'll think of a better system later in the year. I am trying to perfect the recipe for my father-in-law's visit from Sweden in October.
The result is golden, smooth treat. This has been providing the liquid inspiration for my Spineless Songs (see sidebar). The aroma is real nice and the hints of fennel and citrus make it a very pleasurable beverage.