A map of the location of all aircrafts over the USA on Thursday, Sept 27th 2007 at 4pm PST. I bet it looks even worse in the early AM!
Are this many plans necessary? Do we travel too much?
Via the NATCA
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An important step to a better understanding of the adaptive significance of extrapair mating behavior in socially monogamous species is to uncover the identity of extrapair sires (EPS). Here, we used a combination of multilocus DNA fingerprinting and microsatellite analysis to identify EPS in the socially monogamous coal tit (Periparus ater), a passerine bird with high rates of extrapair paternity. We then analyzed how fertilization success was related to male age in 2 consecutive first brood periods based on knowledge of the exact age of the majority of territorial males. EPS were significantly older compared with the males they cuckolded. Furthermore, extrapair and, as a consequence, also total fertilization success were positively related to male age, while within-pair success was not. Interestingly, fertilization success did not increase linearly with male age but leveled off for older age classes and was most parsimoniously described by the inverse term of male age. Results were consistent over the 2 years, while the demography of the study population differed with respect to the age distribution of territorial males. Furthermore, we also show that individual males increased their extrapair fertilization (EPF) success with age indicating that cross-sectional analyses were not confounded by cohort effects. Together with the results from other species, these findings suggest that male age (or a strong correlate thereof) is a major determinant of EPF success in several socially monogamous bird species.
So basically the authors take their knowledge of the demography of the population, use genetic techniques to assign parentage, then compare age and fertilization success.... Not so surprising, older birds do better.... The graph to the left illustrates this point(A and B represent different years).. Points above the 1:1 isoline represent cases when the extrapair sire was older then the social mate. For me anyway, then graphs were not that convincing, but in table 3, they show that there were statistically significant differences in the predicted direction.
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Specifically about the fuss everyone made about his visit to Columbia...
Since when do we believe that ignoring the problem leads to the solution... I for one think that it is great that he was given the opportunity to speak- Remember the saying, Know thy enemy?? People with whom we disagree still have valid points on certain topics... we should be doing a better job of listening!
Has the world really bought Bush's ridiculous philosophy of foreign policy?? See no evil, hear no evil??? Good grief people... we should listed to everybody- it doesn't mean we have to agree with them!
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The goal is this step is to ligate double stranded linkers to each end of the DNA fragments you created with restriction enzymes. The linkers provide PCR primer binding sites for subsequent steps.. It is a pretty cool idea!
1st step is to make the double stranded linkers.. This is easy. Simple mix equimolar amounts of each primer, heat to 95 degrees, and cool slowly. They are designed such that they self-anneal.
Next is the ligation, which is also very easy!
NEB 10X Ligase Buffer | 1uL |
| NEB T4Ligase | 2uL |
| ds SuperSNX Linkers | 7uL |
The image quality is poor- clicking on the image improves it.. something about the way blogger compresses images I suppose...
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Tuesday 9/18/07
Step 2 of the protocol calls for a restriction enzyme digest of genomic DNA. The idea is to chop up DNA into pieces small enough so that they can be easily cloned, but large enough to have a good chance of having a microsatellite AND enough flanking sequence to allow for primer development.
The authors of the protocol use the restriction enzyme Rsa1 primarily, and then BstU1 if that fails.. The recipe is simple -->
| NEB 10X Ligase Buffer | 2.5uL |
| 100X BSA | 0.25uL |
| 5M NaCl | 0.25uL |
| Rsa1/BstU1 | 1uL |
| Xmn1 | 1uL |
So there are a couple of worrisome bands on the 1st 2 lanes labeled Degu, so we tried the BstU1 on that one. The others look OK, with the majority of the smear being between 300bp and 1000bp.
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Monday I started the long process of isolating microsatellites de novo for 5 mammal species.... I'll plan on posting a step by step account of how things are going, so interested people and family can stay up to date. But in addition to this, I hope that this series of posts will serve to fill a small void that exists in the current state of the internet...
For instance, suppose, you do some DNA extraction, and run the resultant genomic DNA on a gel. What is it supposed to look like??? The size distribution of gDNA is a basic measure of the quality of an extraction.... But what is good??? Search the internet currently, and the answer is not easily encountered. This is in contrast to searching for other things (i.e. pornography) where information on the most obscure topics are readily available..
Now more specifically, suppose you are following a well cited protocol, and at each step there is a check, and this check can be run on agarose....but the author doesn't tell you how it's supposed to look.. Now that is frustrating! Why does he give you the ability to check your work, but not the ability to interpret the results of that check? You know that there are other people out there using this protocol (a web of science search shows the protocol is heavily cited), but somehow, a google search is simply no help...
Maybe this is exactly how "open science", "open lab", "open everything 2.0" is supposed to work.. I see that Bora has been a champion of this idea, but I don't see a lot of people heading his words... It seems that these basic types of information should be available... Argh.
Well I will do my part... I will write more as time permits, but for the record, I am using Travis Glenn's Microsatellite Isolation Protocol (PDF). It is a well cited protocol (Cited ~10 times this year). It uses biotinylated oligos (common msat repeat sequences) and Dynabeads for capture... The 1st step- no surprise is genomic DNA extraction. A couple of points:
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So Jeff Wall came to Berkeley today, and spoke to The Department of Integrative Biology on his recent work..
As many of you may be aware, Jeff is a Professor over at the Institute For Human Genetics at UCSF. His recent publication on PLoS Genetics, "Inconsistencies in Neanderthal genomic DNA Sequences", has received a lot of attention not only from the popular press, but also from the scientific community. Last year Johannes Krause (The Greene Paper) of Svante Paabo's lab came to Berkeley to present the Neanderthal DNA sequence data.... He was well received, but there were significant concerns about human contamination... Krause seemed to be confident that they was appropriately dealt with.. I guess not.
So briefly, for those of you not familiar with the Neanderthal DNA "inconsistencies" issue... 2 papers were published last year on Neanderthal genomics. Both projects used the same fossil, carried out similar analysis, but had completely different results....
| Noonan | Green | |
| Modern Human-Neanderthal sequence divergence date | 706 Kya | 560Kya |
| Modern European-Neanderthal Population Split | 325Kya | 35Kya |
| Neanderthal Contribution to Human ancestry | 0% | 94% |
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Welcome to the 88th edition of the Tangled Bank, the best and longest running science blog-carnival out there. For the newbies, we blog about science, casting a wide net over the physical, social, and life sciences. Anybody is welcome to submit, so long as it is about science. This weeks posts come from as far away as 
enjoy the carnival, there are some really nice posts. Before you leave, make sure and check out the Behavioral Ecology Blog. Oh yeah- vote in my poll...---------------------------------->------------------------------>
1st on the list is the GrrlScientist, who tells us about a scary-creepy place Texas, where a very large group of spiders has transformed a park into a haunted house in a post entitled “Spiders Spin A Web the Size of Texas” BREAKING NEWS from the Grrl- Alex the Parrot has Died..
Hsien is at it again, posting about the Wellcome Collection which is a Museum owned (sponsored? managed?) by James Watson who BTW will be speaking in 
Guys: Imagine an infection that might:
Horrible huh, too bad such an infection exists.. go read about it over at Evolgen!
Invasive Species Management is big business, and rightly so. The management of invasive species (plants and animals) cost taxpayers millions of dollars yearly, and inflict irreparable damage on ecosystems. While there are clearly plants that behave like invasive, plant behavior occurs on a continuum, with some plants clearly invasive, others clearly not.. What about the majority of introduced plants fall somewhere in the middle? Turns out, there is an objective method used to score plant behavior… GreenManTim gives us the gory details on how this is all worked out over here.
While GMT’s post deals with the politics of invasive species, Jennifer describes for us the daunting task that is their removal from a particular place over at her blog in a post entitled “Tower Power”
Screwworms are one of those animals that have to power to mystify, intrigue, and horrify all at one time.. They are one of the most magnificent parasites out there- unless you have them of course. Well…. You say you don’t care for them, you’d rather not have them huh- turns out there is a non-eco friendly way to get them out- irradiate the males of course.. Read about the poor sterile makes over at Discovering Biology in a Digital World.
I’m not sure how he has time, but Brian over at Laelaps wins the award for longest post.. Never fear though, while long, it is far from long winded. The post (Convergence or Parallel Evolution) draws from his experience at the AMNH and their sometimes peculiar arrangement of specimens and gives us a nice primer on evolutionary theory.
From a grad student at a Big Ten school with a Football Team that is not 0-2 (
recently. The 2nd is something about chirality and snails.. Reminds me too much of my organic chemistry days to say more..
Brains are pretty cool, and are somehow related to “being smart” says Alvaro over at SharpBrains. He says that it’s all related to the accumulation of patterns- seems pretty reasonable to me… ON another note, a 2nd submission contains a list of cool quotes from Neuroscientists. I guess I get a little uneasy when powerful scientists support particular ideas with anecdote, but here it is.
You know that parasites rule the world don’t you?? Well it is true.. Over at Science Made Cool, one particular guy, North American pine wood nematode (Bursaphelenchus xylophilus) is described.
Have you ever wondered what makes people great— people like Copernicus, Bruno, William Harvey, Tycho Brahe and Kepler. How do great scientists come to be anyway? I sure don’t know, but turns out someone does- and has written a book about his findings- do read the review over here…
As some of you people may know- I’m pretty short. So short that my Dad considered subjecting me to growth hormone treatment when I was a kid. In retrospect, I’m pretty glad he didn’t, as I’ve come to know the benefits of being short (think dancing with taller girls). Anyway, it has come to light that there is a gene that is responsible for some of the variation in human height- curious? I sure was.. So go over and read up on Greg’s blog in a post fitly entitled “Tall Gene”
I’m not quite sure what Archaeozoology is, but if this post is representative- I want to know more. Infectious disease, volcano's, old-burnt people, and how they are all related is whats in store for you with a click on this link!
Rotten tomato or Kumato™, you decide….
I’m not sure who Ol’ Sam Peabody is, but if he is a sparrow, as an east-coaster, I’ll agree… Trash Bird. You’ll easily see 100 of these visiting virtually any park…. Despite my personal opinion about these guess, you can’t deny that they are actually really pretty, which is illustrated quite nicely by a submitted post over at 10000 Birds.
Apparently Professor Steve Steve likes Peyote, a substance I thought was banned for use in
stuffed pandas…. That not withstanding, it looks like he WAS having a pretty good time over in
A bunch of really interesting blog posts surrounding the question “What is Life” have been circulating… A discussion on the necessity of a useful operational definition and a summary of key contributions is yours over at BioCurious.
This week’s winner for most submissions is Eric Michael Johnson with 3. Too bad they are all
SUPERB! I’ll highly recommend them all..
Lastly, there several posts that I have found to be particularly interesting.
- A guide to translating scientific papers into plain English.. REALLY FUNNY (AND TRUE)
- J Craig Venter, thoroughly exposed.
- An update on the crazy Texan spider story.
- Are species theoretical objects?
- Will climate change shrink mans manhood, too?
OK, it’s time for you all to go home, but before you do that, check out the rest of my blog, and subscribe to my RSS feed if you like what you see… Make sure and start saving up posts for next edition, which will be over at Aardvarchaeology in 2 weeks. Please let me know if I forgot somebody, or if links don't work...
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Here are some quotes from the loser coach and the talented running back.. Notice the difference in accepting personal responsibility?
Michigan's Coach Carr:
On if this is the most difficult start to a season in his career .... "I don't think we could have a more difficult opening than we've had. We had tremendous expectations, yet we're 0-2. We did some positive things I thought today in the first quarter. As I look back at it offensively, we knew we were going to have to score some points because Oregon is an outstanding offensive football team. We turned the ball over again and couldn't sustain some things and missed a field goal there that hit the uprights. We gave them 21 points on big plays. The foundation of your defense has to be you can't give up big plays, and offensively you have to find a way to win the turnover battle, and we did neither of those things today. We just didn't get it done offensively or defensively."
On what he's been most disappointed in through two games ... "We didn't tackle well, and some of that I attribute to outstanding running back play. Certainly, if you're a defensive team that gives up big plays and doesn't tackle well -- and we're not tackling well, we're not excusing that -- we were unable to make some of the tackles when we were in position. They bled us for six or seven or 12 yards instead of three or four, which sustained their drives.
"I thought offensively (on the first drive) we took the ball and put a real good drive together and then we made a bad throw that got intercepted and was run back for 50 yards or so. Then we held and put together a great drive. We started off, I thought, very well. You're going to have to score points against Oregon. We just have no consistency. Of course, Carlos Brown went in and played. Mike Hart had very, very few practice plays this week. Brandon Minor didn't practice at all, and Carlos got some practice time. (Carlos') hand is very close to being back. That turnover really took some wind out of us."
On where the team is from an injury standpoint ... "A lot of guys were dehydrated. It was really muggy down on the field. I don't know how long it was in duration, but there were a lot of snaps on both sides of the ball. We had a lot of guys cramping, as did Oregon. We'll just have to see tomorrow and Monday how the injury deal is. It will be what it will be. We just have to go on. I think (quarterback) Ryan Mallett got some good experience today."
On what he will talk to the team about going forward ... "I told the team after last week's game what was going to come our way. I also told them that there is tremendous support out there for them as players from people who truly love Michigan. It's not like they don't have any support because they do. In my judgment, the battles we have to fight are confidence -- we have to do a good job working hard in practice. There is no magic bullet. There is a lot of work that we have to do. We have a lot of young guys that need to improve. I think that we have the leadership on this team. Mike Hart, Jake Long and Chad Henne gave up the NFL to come back here. They're not going to give in. They're going to work hard. What we have to do as a team is stay together. As long as we do that and play our hearts out then at the end of the day we can look each other in the eye and know we didn't give in, back down or bow down to anybody."
On why the team is 0-2 and what stopped the offense today ... "We just haven't come out and played. We haven't followed the game plan. We haven't been out here just finishing. If you look at the offense today, we punted the ball one time in the first half and that's because we had a delay of game. Obviously, they really weren't stopping us. We were stopping ourselves once we got inside that 30-yard line. In the second half we didn't come out and play, period. I just don't think we came out and played."
On who else needs to step up their game for the team to succeed ... "Everyone needs to step up. When you're 0-2 everyone needs to step up. I don't expect people to do what I do. We have young guys. Everyone is not Mike Hart, everyone is not Jake Long, everyone is not Chad Henne. We are the guys who need to step up -- we're the playmakers on this team. When playmakers step up, people are going to make plays. Playmaking is contagious. If we start making plays the younger guys are going to start doing it. People are going to be enthusiastic. The young guys are going to block better. We're not going to have those mistakes. So when I say I need to step up, that's why I need to step up."
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"Maybe" I suppose is the best answer I can give right now.. What we do know is that there is a strong correlation between industrial pollutants and shrinking polar bear dong's. Now Ursids are not exactly "close relatives", but they are mammals, and many of our physiological processes are identical... I bet the experiment done on humans would yield something similar (but think of those poor guys who volunteer for this study). Of course this is me crossing the causation/correlation line a bit...
Sonne and his colleagues looked at formaldehyde-preserved genitals from 55 male and 44 female east Greenland polar bears, collected from 1999 to 2002 by about 30 polar bear subsistence hunters regulated by the Greenland government.The adult polar bear testicles the researchers examined were on average roughly three inches across and 1.8 ounces in weight, although they could dramatically enlarge during the height of sexual activity from January to July. Their bacula, or penis bones, were on average nearly seven inches long.
The scientists found the higher the level of organohalogens*** in polar bear, the smaller testicle and baculum size and weight likely were. Ovary size and weight decreased as organohalogen levels rose as well.
Maybe even worse, the authors suspect that,
In fact, all marine mammals could get affected by these pollutants, "especially the Arctic fox, killer whale and pilot whales,"
But who cares anyway?? The problem is this, that while human males use their phalli for "pleasuring" females, most other mammals use them to stimulate females.. Only a properly stimulated female will consent to mate.. Basically, you might have the situation where there are receptive females that can't find suitable mates... So add this problem to the already very slow rate of reproduction characteristic to polar bears, the receding polar ice sheet, lack of prey items, and active hunting and you have a species that is in BIG trouble..
So what does this mean for Homo sapiens?? Well for me, it means the loss of one of the most beautiful animals there is.. not to mention a top predator, indicator of ecosystem health, etc.. Just imagine how food webs, and general ecosystem function will change... It's not likely to be pretty... Now I don't eat much marine mammal meat these days, but what about all the folks that depend on these mammals for sustenance.. watch out guys, they're comin' to cut off you man parts... Those poor guys, they 1st have to see the animals die off, then endure ecosystem change, they can't eat the stuff they are used to (unless they're OK with the risk of shrinking penis syndrome), and to add insult to injury, WHILE THEIR PENISES ARE SHRINKING, THE MEN CAUSING THE PROBLEM ARE GETTING BLOW-JOBS IN AIRPORT BATHROOMS...
I wonder how quickly politicians would take meaningful action to combat global climate change/pollution if their genitalia was shrinking??
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Ron English.... GET OUT OF MICHIGAN.. oh yeah, you too Lloyd Carr. How long is it going to take you to figure out spread offense and mobile QB's... Every team we play knows how vulnerable we are to it.. solve it, or GET OUT!
Just in... Michigan turns over the football AGAIN.. It is likely to be a long day... My head is already hurting....
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It's that time of the month again where you get to send in interesting, exciting, weird, or otherwise noteworthy science stories for inclusion to the next edition of the Tangled Bank blog carnival. Feel free to send them to me, PZ or host@tangledbank.net before Wednesday, 12 September.
See the most recent incarnation over at Balancing Life.
While your here, why don't make sure you won't miss it by subscribing to my RSS feed.
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Smelled smoke from the Huge Plumas Fire this evening... The fire is hundreds of miles away, but the smoke plume is massive... See the photo.. The red boxes in the upper right hand side of the photo is the fire, and all the smoke is, well, the smoke. Note that it extends all the way down to the San Francisco Bay... Note the Lick fire, tiny in comparison is in the lower part of the image- also in red...
Go find you own cool image over at Nasa's EarthObservatory.
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Has anybody else had this experience???
I tried to upload a video- I stopped it after it said it was processing (and wouldn't let me publish) for over 6 hours... The video was 6MB. Google video took <10 minutes to upload and process..
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"This mechanism of prey transport is behaviourally and functionally convergent to prey transport in snakes. Snakes transport prey by alternating ratcheting movements of the left and right sides of their upper jaws to advance their head over prey12, 13. Oral jaw ratcheting is coupled with flexion and extension of their cervical and thoracic vertebrae13. Ratcheting enables snakes to maintain a bite on their prey with one side of their upper jaws while the opposing side moves over the prey. Morays transport prey using alternating movements of the oral and pharyngeal jaws followed by flexion and extension of the anterior region of the vertebral column. The dual-jaw system of morays functions to alternate oral biting with pharyngeal biting, allowing morays to maintain a grip on their prey at all times, as snakes do."
Basically, she found that while most Telosets feed by using suction in some way morays are poor suckers. Instead, they grasp prey with their outer jaws, then the pharyngeal jaws — which normally sit behind the skull — reach forward into the mouth to grasp the food and carry it back for swallowing. What the heck is a pharyngeal Jaw?? Here is the photo..
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This is Owego, NY circa 1985. I grew up here... The cars are different now- but the storefronts are largely unchanged...
Here is a high-rise being built in La Paz, Bolivia.. How many code violations per US standards???
Lauren (My eldest Daughter) eating tin-foil- and playing with a skull....
Yes, I was a hockey fan even back then...I wonder why I let my younger sis wear the Canadians shirt??
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Yeah, your right.. maybe still too advanced
via MCS
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Here is a map of the percent of average precipitation from January to the end of July... >20% of usual rainfall in the vast majority of Southern CA... exactly where my field site is...
The mice have not bred this year, and populations are very low.. I'm not sure that even A wet fall/winter will revive them.. The relationship between rainfall and reproduction is an interesting phenomenon yes, but not when the prospective title of your dissertation includes the words "mating" and "Peromyscus", and they aren't mating at all...
I wonder how Texas, and the Midwest in general got so lucky with the rain..
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A hilarious video about the Farm Bill that includes a fight between an apple and a Twinkie... I only post it because we were in in attendance for it's making- at least the part filmed at the Berkeley Farmers Market..
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There is no doubt that in Coach Carr's prime, he was a great coach. Great for Michigan, and great for College Football.. But those days are over.. He has repeatedly failed to prepare the team both physically and psychologically for beatable opponents.. Today's disgraceful loss is simply the latest in a long string of examples...
Per Lloyd:
"We were not a well-prepared football team," Carr said. "That is my job, and I
take full responsibility."
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