Saturday Summary #2

I know it is Sunday but hey I'm still recovering from the Montana win in the Brawl of the Wild, now they are seeded #1 in the FCS playoffs - although South Dakota State is going to be a difficult opponent, so I'm not sure the seeding committee did them any favors.

OK, so this week was pretty good - not great but good. There were no mechanical issues to speak of cars or other wise - although we do need to keep the car under a certain speed limit. S was out sick for three days, but he didn't miss much, I'm pretty sure the teachers were looking forward to a week off as well. L made it to her 9 mos birthday, now has two teeth, speed crawls everywhere, stands up at will and well pretty put everything she can pick up in her mouth. This causes Mom, Dad, and siblings to be super vigilant.



Work was pretty good, submitted a grant and finished one of the paper revisions I've been working on. This week, is Thanksgiving and I'm trying to get more revisions done for another paper. Have a great week.

The Friday Five #1

Here is a list of 5 articles and new items that caught my interest this week.

1) Explaining the Linguistic Diversity of Sahul Using Population Models An interesting way to look at the evolution of a language and their relationships. Hopefully, in the future they could investigate whether genetic information overlaps with the linguistic boundaries using the same type of information. They apply the program Structure and if you had a significant number of SNPs/STRs perhaps you could determine a statistical relationship between these to determine if there was co-evolution.

The region of the ancient Sahul continent (present day Australia and New Guinea, and surrounding islands) is home to extreme linguistic diversity. Even apart from the huge Austronesian language family, which spread into the area after the breakup of the Sahul continent in the Holocene, there are hundreds of languages from many apparently unrelated families. On each of the subcontinents, the generally accepted classification recognizes one large, widespread family and a number of unrelatable smaller families. If these language families are related to each other, it is at a depth which is inaccessible to standard linguistic methods. We have inferred the history of structural characteristics of these languages under an admixture model, using a Bayesian algorithm originally developed to discover populations on the basis of recombining genetic markers. This analysis identifies 10 ancestral language populations, some of which can be identified with clearly defined phylogenetic groups. The results also show traces of early dispersals, including hints at ancient connections between Australian languages and some Papuan groups (long hypothesized, never before demonstrated). Systematic language contact effects between members of big phylogenetic groups are also detected, which can in some cases be identified with a diffusional or substrate signal. Most interestingly, however, there remains striking evidence of a phylogenetic signal, with many languages showing negligible amounts of admixture.

2) Pre-Eclampsia Linked to Thyroid Problems: This is an interesting news item from Sciene Daily that demonstrates a relationship between Pre-Eclampsia to hyperthyroidism. I have some personal interest in this so found it intriguing.

3) Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide Analysis: A GWAS study that rather than just look at the major lipid phenotypes (i.e, HDL-C, LDL-C, etc.) breaks them down into different size phenotypes to get greater resolution.

While conventional LDL-C, HDL-C, and triglyceride measurements reflect aggregate properties of plasma lipoprotein fractions, NMR-based measurements more accurately reflect lipoprotein particle concentrations according to class (LDL, HDL, and VLDL) and particle size (small, medium, and large). The concentrations of these lipoprotein sub-fractions may be related to risk of cardiovascular disease and related metabolic disorders. We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women's Genome Health Study (WGHS). Among 36 loci with genome-wide significance (P<5×10⁻⁸) in primary and secondary analysis, ten (PCCB/STAG1 (3q22.3), GMPR/MYLIP (6p22.3), BTNL2 (6p21.32), KLF14 (7q32.2), 8p23.1, JMJD1C (10q21.3), SBF2 (11p15.4), 12q23.2, CCDC92/DNAH10/ZNF664 (12q24.31.B), and WIPI1 (17q24.2)) have not been reported in prior genome-wide association studies for plasma lipid concentration. Associations with mean lipoprotein particle size but not cholesterol content were found for LDL at four loci (7q11.23, LPL (8p21.3), 12q24.31.B, and LIPG (18q21.1)) and for HDL at one locus (GCKR (2p23.3)). In addition, genetic determinants of total IDL and total VLDL concentration were found at many loci, most strongly at LIPC (15q22.1) and APOC-APOE complex (19q13.32), respectively. Associations at seven more loci previously known for effects on conventional plasma lipid measures reveal additional genetic influences on lipoprotein profiles and bring the total number of loci to 43. Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism—including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles—all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay.

4) Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico: An interesting look at the mtDNA mutations through the aging process.

The mitochondrial free radical theory of aging (mFRTA) implicates Reactive Oxygen Species (ROS)-induced mutations of mitochondrial DNA (mtDNA) as a major cause of aging. However, fifty years after its inception, several of its premises are intensely debated. Much of this uncertainty is due to the large range of values in the reported experimental data, for example on oxidative damage and mutational burden in mtDNA. This is in part due to limitations with available measurement technologies. Here we show that sample preparations in some assays necessitating high dilution of DNA (single molecule level) may introduce significant statistical variability. Adding to this complexity is the intrinsically stochastic nature of cellular processes, which manifests in cells from the same tissue harboring varying mutation load. In conjunction, these random elements make the determination of the underlying mutation dynamics extremely challenging. Our in silico stochastic study reveals the effect of coupling the experimental variability and the intrinsic stochasticity of aging process in some of the reported experimental data. We also show that the stochastic nature of a de novo point mutation generated during embryonic development is a major contributor of different mutation burdens in the individuals of mouse population. Analysis of simulation results leads to several new insights on the relevance of mutation stochasticity in the context of dividing tissues and the plausibility of ROS ”vicious cycle” hypothesis.

5) Family Plans: a blog post from the people over at Science Careers that looks at the number of people looking to begin families while still in "training" either as a grad student or postdoc. I found this interesting as that my wife and I had 3 kids while in grad school and I've had one as a post doc. There was a certain amount of flexibility that came along with having kids in grad school, which is not as easily accomplished post graduation. For another interesting perspective check out Freethinker's Asylums recent post on Finding Balance.

Saturday Summary #1

I thought I would start a new blog post series today and kind of run down the past week, it beats having to do it once a day and occasionally on Saturdays I have a few extra minutes to actually write at the computer. First off today is C's third birthday. It doesn't seem that long ago that we were bringing her home from the birth center in KS. Wow, she is definitely my most independent child and lives up to her namesake from King Lear. Today, she got cupcakes for b-fast, to go out to lunch, and go to a park. We will have a joint C-X-J b-day in a couple of weeks.



The other big thing to happen this week was the brakes on our one working car went out. So J spent 7 hours at the brake shop getting them fixed. However, they did tell them how to fix the other car cheaply so hopefully we can get two cars again so it will be easier to get around. Grr for car trouble.

Work was a little better, I got a grant in and submitted so that is good and I'm working on some revisions for another paper, which should be done by Thanksgiving, then some other edits by Dec 1. and finally a new draft by X-mas or at least that is the plan.

Resolution Roundup #10 - October

So once again I've been neglecting my blog following (thanks to all four of you and you anonymous ones as well). This month has been pretty hectic. The month started out with a visit from my nephew. Thanks for coming A - the other day X said he missed him. Then I spend a week in Hawaii at two conferences (oh the stress of working), followed by the excitement of Halloween and through about four or five birthdays and a few colds into the mix and it allows for very little computer time. Here are some pics from Hawaii and also from Halloween.


A View from the room at Turtle Bay Resort, where IGES was held (very cool conference). I presented a poster on fine mapping of the Hepatic Lipase gene, which is involved in HDL-cholesterol metabolism. I also gave a poster at ASHG on a potential gene involved in Heart Rate located on chromosome 9p21 (which is a very interesting genomic region that appears to be heavily involved in heart disease).

Cordy went dressed as an orange witch - J made the tutu and all cool witches were Chucks.

X went as the ninja assassin - he still hasn't put the sword down - even though he did almost poke my eye out with it while playing a rousing game of pirates on the bed.

S went as a fluffy dog for the second year running, we've gotten a lot of mileage out of this costume that was given to us by J's bro and sis-in-law.

Anyway here are is the resolution roundup for the last month.

• Volunteer - This remains a pipe dream and will probably get carried over into next year.
  

• Pay down debt - Similar to last month - we are still trying to get back on track. We are also trying to sell the house in KS - so anyone moving to Lawrence - let us know.
  

• Be a more patient father - I'm still working on this but I need to get back into a more structured groove. The fam is out of sync due to a number of things - adjusting to a single car and Spencer's school schedule makes it somewhat difficult to maintain some flexibility in the schedule but we are working one it.
  

• Read two books a month - Once again I read three books this month and once again all by Steve Berry (see below). Now only one more novel and I will be done. This month it was pretty much a tie between the Third Secret and the Romanov prophecies as far my favorite goes. However they are all good. Next month I will probably return to more of a pulp noir phase or at least until I get my hands on the upcoming Steve Berry book or Dan Brown's new novel.
  
  


• Publish, Publish, Publish - Here is the status of this right now. I'm working on three revisions and one is out for review. Then I have two more I'm drafting right now. However, I plan to tone this down a little bit and get some quality manuscripts out in the next year as well as right more grants (which I should be doing right now).
  
• Be a more substantive blogger - One day I will return to blogging when life is less chaotic and I invent a time-stand-still machine.
  
• Take a vacation - Hawaii was a success and I will go back with the family, when the kids are older so they can remember it. Next years looks to a busy travel year with trips to KS, NM, DC, and MA in the works so very busy and productive time.
  
• Find a hobby - Is navel staring a hobby, do I have time - maybe I should just read comics. The garden is back up with some new food (broccoli) as the weather has morphed into extremely pleasant - no wonder I like Texas
  
• Spend one on one time with my kids every week - We've got the bedtime routine down and I enjoy reading to them - now if I could stay awake past 8:30 I would be doing good as well and maybe I could have a conversation with J. The boys are addicted to PBS kids online games - it is amazing how well they can navigate that site. Now when the sugar high breaks down hopefully they will be a little less crazy.

Until next time ...

Quote

I'm not sure where this came from but fairly accurate.

"A sufficiently trained statistician can read the vagaries of a Q-Q plot like a shaman can read a chicken's entrails, with a similar recourse to scientific principles"

The Morning Traffic Dragon

Every morning on our way to drop off S at school and then me at work there is generally significant traffic (with no traffic it takes approx. 15 min to get to work whereas with traffic it can take 30 min to 1 hour and don't ask about it if it is raining). Anyway the long line of cars backed up always reminds me of the dragon from the 13th warrior. This is a distorted view but I thought it looked more dragony.

The Lost tribe of SA

Just realized I hadn't thrown up some pictures of the wee ones lately. Well here they are in their natural habitat (i.e. the backyard). They even took L outside to see what nature was (we know Mom is anti-outside but she did take the pictures). These kind of reminded me of the lost tribes of the Amazon pictures (staged BTW) from last summer.

Being forced to eat Mickey Mouse, while C wards away the camera.


Overseeing the annual laying of the going to school quilt.

Hey, where did everyone go. I can't walk here people.

Resolution Roundup # 9 - September

1. It is that time of the month and I realize that I have been neglecting my handful of blog followers. Life in Texas has been cooling down while work has been heating up, hence the absence. Anyway here is how September shaped up with the resolutions. Also, we are adjusting to Spencer going to school and the Mini-van croaked out on us so we are down to one car, which makes travel around the eighth largest city difficult sometimes.

• Volunteer - This is not a matter of procrastination on my part but a matter of time. I generally work 9-10 hours then go home, eat, get the kids to bed, fall asleep myself, wake up, wash, and repeat.
  

• Pay down debt - We need to get back on track with this, we are behind on a few things and and I hope to get got caught up here shortly. J has also started marketing wine - so here is a shameless plug for her web site Time Out Wine. She also writes article for the San Antonio Examiner and gets paid per click. So check her out, buy some wine and read about attachment parenting.

• Be a more patient father - We are working on this, I tend to have high expectations for my kids and sometimes I may treat them like they are older than they are actually are. This is especially true of X and C as they are both pretty bright -so sometimes they are really smart. I suppose parenting is a learning process and I should enjoy the ride sometimes.

• Read two books a month - I read three this month all by Steve Berry (see below). I have to admit I'm really enjoying reading guilt free fiction. All three of these books are good reads although my favorite so far is the Alexandria Link. What happened to the scrolls from the library at Alexandria, is the Old Testament accurate or is it a misreading of Old Hebrew and Zion is really in western Saudi Arabia. You can pretty much put Templar in the title of any of your books and I will read it. I'm fascinated by the Templars, Philip the Fair, and Jacques de Molay. Heck I even named my Fantasy Football team the Templars (they have a cool logo). The Venetian Betrayal was excellent as well, about Alexander the Great. I'm currently reading the next book in the series and can't wait until the new one comes out in December.
  

• Publish, Publish, Publish - Here is the status of this right now. One is in major revision, two are out for review one of which I'm first author and another as second author, another is being modified into a short report and submitted as a skeleton of an article. I submitted two more abstracts this month. So we will see how this works out. I submitted a grant but it didn't get funded even though it had a good overall score and the reviews were positive but the budget was a limiting factor for the scope of the grant.
• Be a more substantive blogger - This is still in limbo but I have some good ideas but it Football season - c'mon here I have a Fantasy Football team to look after.
• Take a vacation - I'm off to Hawaii this month, then Kansas in March, then New Mexico in April but these are all work so I need to plan something close to home - maybe a trip to the beach next year.
• Find a hobby - I've been thinking about the garden. I think we are going to do flowers and maybe some herbs - surprisingly J's Aloe plants lasted the summer outside. So we will start small then work are way up.
• Spend one on one time with my kids every week - We are going to attempt to formalize a bedtime routine at this point now that we have taken back the TV from the monster channel that is Cartoon Network. The boys learned how to use the remote and it took us weeks to figure out how to block the channel - way to make that smooth Time Warner. I do enjoy spending time with them a little every week. Today X and I are going to go for a walk around the neighborhood - this may be a good way for me to connect with each of them individually.

Well until next time I decide to blog adios.

College Football

College Football season is upon us and for the first time in a long time I can actually watch it unencumbered by the stress of school. I have no idea what football season will be like, it has been so longs. Not feeling guilty about sitting in front of a couch for two hours eating junk food and yelling at the TV. I can now reclaim TV viewing for a portion of the weekend and realize why I pay a boatload of $$ to Time-Warner.

The season got kicked off last night and those of the Smurf Turf (Boise State, see below) beat Oregon. So a non-BSC (Bowl s*** Champion division) beat a Pac-10 team that was supposed to vie for the top spot with USC, ha. See now if BSC football had a playoff system (like my favorite team that has been to the championship game six times) like every other sport known to man or alien then I might care. Go Griz!

Chubacabra or Not Chubcacabra

It would appear that every year that some hapless Texan captures a mexican hairless dog and equates it to being a Chubacabra. Last year the KC Star reported the capture of chubacabra - that sucked the blood dry of a bunch of chickens and now this year Yahoo is pimping this news item that they stole from CNN. It's a flippin canine people, large but dead and baked in South Texas. Chubacabras don't exist, they are myth like Bigfoot. I have no idea why a media outlet would run a story without verification, oh yeah - they no longer do journalism they read the internet.