Week 75 - Cold

It was officially bitter cold out last week. There is snow on the ground, the winds have ripped the loose branches and resistant leaves from the trees and there is no cloud cover. Clear nights, ripping wind and bitter, bitter cold. With windchills reaching below -35F, I can only remember one other week in my history that was so cold. Spring semester of 2007, early February.

View from my dorm in 2007 with the sun trying to cut through the snow.

My walk to class in 2007. -45F but classes weren't cancelled, just the bus routes.

Well, this time around we were blessed with class cancellings and delays for work, but that was really last week. I still went to work to finish my proposal and get it turned in. What matters this week is that the cold hasn't really broken and the wind certainly has not. With temperatures in the single digits and windchills fluctuating from nothing to -30F, we have seen a few 60+ degree shifts in the past week or two. So when the sun broke out when my wife and I were headed home from a birthday party, we drove home as fast as possible to get the camera. It felt so warm with the sunlight streaming and the wind lightening - or at least it felt warm for a few minutes. My wife has the better pictures but when she got cold I ran out on the edge of the lake and tried to catch the snow that was floating across the ice. It looked like the fog from dry ice as it swept towards me, and with the sun dropping fast with its diverse color palate, the scene was an eerie reminder that this break in the weather is only a break. The winter storms will return.

Silhouette of my wife walking to another spot for pictures on the lake.

The color paling as the sun disappeared.

Hannah is finally up to her knees and working on her ability to stand up! It's so funny to see her sitting back on her knees. She looks so comfortable, as if she has always just been sitting back on her heels waiting for people to play with her. Sitting up from laying on the floor is still a challenge, but she has found the work-around by rolling and grabbing things around her. This also means she has become a bit more interesting to Betsy. Now that the baby in her life seems to be more like a human, Betsy seems to think that she is just a human puppy here to play with her. We have to be careful to make sure that Betsy doesn't paw at Hannah, because she doesn't mean to hurt her but those claws can scratch her if we aren't careful. Of course, Hannah doesn't care. She just loves Betsy sitting so close to her and sharing her toys and food with Betsy. The two of them will be an inseparable pair in just a couple short years.

My Spartans may have had a great year in football, but it seems to have come at the cost of offending the basketball gods. Just when I thought we had suffered enough injuries for one year, Dawson is sidelined with a broken hand. And get this, his hand was broken because he punched a table!! Now, for most of you Dawson doesn't mean a thing. Even some commentators said it wasn't as big a deal as some of the injuries. But Dawson is the catalyst. In my field, we talk about catalysts as the thing that speeds up the reactions, maybe making them viable in otherwise limiting conditions. But in this case, Dawson is the spark (maybe activation energy would be a more appropriate term). He lights up the team and puts the fight in their eyes. He knows what it means to win and he knows what it means to have the game taken away from you. Lately his fire has been lacking, so I can only hope that at least with this energy he will return with renewed zeal for the game. Like Boeheim said about the 'Cuse/Duke game, "It's all about the game," - love of the game.

My proposal was completed and mailed out to the committee at the end of last week, giving enough time for people to send in comments or corrections before the candidacy exams. I know that many people struggle with the amount of corrections, but I received none. Granted, I had already worked extensively with a grant writing specialist in our department, and passed the concepts by my advisor. But out of the other three committee members, I received only one person's written comments and they were minimal. That leaves me just a bit uncomfortable as we approach the written exams. So I am just reading up on the previous work done by my committee members and trying to keep my head in other work so that I can remain calm. Writtens are scheduled for Jan. 30th (my advisor), Jan. 31st (microbiology), Feb. 3rd (modeling and nutrition) and Feb. 4th (statistics and science). It's hard to believe that in only a few days it will be over. I am either going to be acceptable or not. I guess in the end I am not worried about passing. My advisor had me over to his house on Monday and took the time to ask me a lot of questions over a couple beers. He helped me pinpoint things I was weaker on and gave me a bit of coaching on how to answer questions more efficiently. He said not to worry, but then asked me to impress him. So I'm not worried about passing, but I am worried about being a disappointment. Throughout my academic career I have found myself raised on a pedestal and in my undergraduate I am confident that I did not impress my advisors at all. In my masters, I always felt as if my work didn't excite my committee or impress them like I had hoped. So this is my last chance to leave a lasting mark. And the bar has been set high. I just want to make my advisor proud to have me as a student.

Week 74 - Postage

I registered for the Pelotonia this week. This will be my fifth year riding in the cancer research fundraiser and the ride has become more meaningful every year that I participate. Last year, we were connected with cancer patients at the OSU James Cancer Research Hospital and the stories that I learned from current and former patients at the hospital were very moving. This disease debilitates and causes agony in families, and our ride helps find treatments and preventative measures to improve the prognoses of the future. My bike ride may be short and my suffering on those hill climbs is brief; it is a small bit that I can do for those people in my local and global communities. If you read this blog post I don't ask for much, but please go to my profile (click here!)and donate $1. Every dollar makes a difference for the families and patients that are praying for hope and a cure.

I ride so that this little girl can grow up without fear of cancer.

This week we started the final experimental period of trial C035. Our visiting researcher is not coming until next week, and I regretfully started up the trial even though I need to be preparing my proposal and gathering materials for my candidacy exams. We are currently in the process of getting my committee approved by the graduate school which requires a petition to have a committee member not from here, a petition to have the committee member video conference rather than fly across the international date line for the exam, and a standard form to have the committee approved. I like all the resources at this huge institution but the bureaucracy that comes with it is a royal pain in the - well, you get the idea. And my proposal also needs to be completed this week and sent out to my committee so that they can approve it and start preparing my written exams. So yes, I was a little hesitant to start this other trial up but I really need it to be done and a few people in our lab said that they could help out as needed. My advisor says that I'm good at juggling. What he doesn't know is that I'm just good at making things work under pressure.

Part of the trial we are running right now involves the use of IV pumps to infuse isotope-labeled VFAs in a saline solution. As such, I've become a recent pro at hooking up IV pumps and fixing flow issues (when in doubt hit the power button and force it to start over). But I want no part in loading up the isotopes so they had to be mailed to us from Virginia. Well, early this week we received a box with a record number of forever stamps I have ever seen on one package. Fedex would probably have been cheaper. You can count for yourself but I think it was something like $18 in mother Mary stamps. Our lab manager said it best, "He must've really wanted it to get here because that's a hell of a lot of 'Hail Mary's'".

The only good news at work this week was that I got my desk cleaned last week. So as I get knee deep in this proposal I at least have some space to toss stuff around and organize my train of thought. That, and I have been making good on the coffee mug from Starbucks that my wife gave to me. The deal that came with the "January" mug is that I get a free cup of coffee from Starbucks every day in the month of January. And I haven't missed a day. I may not be able to sleep much but the coffee is fueling the madness and at least getting me through the work day. I received a lot of great gifts for Christmas, but this mug was very thoughtful and I think of her every day when I get my coffee before work. Just wishing to be done with this proposal and candidacy so I can be back at home with my family.

Week 73 - Class

No pictures this week as we enter into my posts from January (I'm getting closer to being caught up, and as promised the ship will be righted by the the end of spring break).

Well, this week was pretty brief. I basically show up at work, dive into reading a ton of PDFs, cuss out my Adobe Reader because it always crashes when I load more than 10 files, and then forget to eat lunch. Sometime in the afternoon, I get hungry, eat my lunch by 3 or 4 pm, and then continue reading and try to get to a stopping point. My wife is a saint for taking care of Hannah and supporting my studies. With this funding application I am turning in, one of the requirements is that I have my candidacy exams completed by February 20th. This date is sneaking up on me quicker than I'd like to admit and so my time is divvied into reading manuscripts to prepare my proposal, reviewing pathways for main nutrition, growth and health signaling in livestock, and recruiting members of my doctoral committee. I think in many fields of study, this last-minute recruiting would be more difficult but my faculty members already know me pretty well and are quite willing to be a part of the committee. So far, I have three members for sure because they will be submitted on the grant and agreed back in December and I need to secure one more.

A lot of people have asked me if I'm studying for my candidacies. I've never been known for studying and I'm not about to start now. I call it studying, but what I really do is try to look at the big picture. What systems influence others? What are the bigger concepts of dairy nutrition related to my work? If my committee asks me to defend my ideas, where did I get them from? How can I use my knowledge of statistics to solve problems? But in the traditional impression of studying as a memorization of notes over years of classwork, hell no I'm not going to do that. If I don't know that stuff now, there's no way I will memorize it by next month anyhow. It's more important for me to be able to relate my work to the real world and to cite relevant literature. So I'm basically turning myself into an encyclopedia of manuscripts in nutrition and methane research.

One thing that came up when we had conversation about me taking my candidacy exams was the need to take one more class, another microbiology class taught within our department by a professor on my committee. I was hoping to take it last year but it was cancelled for lack of enrollment. So I'm enrolled in one, yep count 'em, class for this spring semester. And it's been about a year since I took any classes. It feels so weird to have a schedule and I had to set an alarm reminder on my calendar just to remember to go to my class upstairs.

I think our professor was a bit worried that some students were hazy on the old details from microbiology classes so our first week has been a review of basic microbiology. One of those things was gram staining. For those of you who don't know, gram staining basically entails staining bacteria with one stain, then washing it off and adding a different one. Gram positive bacteria have a thick cell wall that will retain the first stain whereas gram negative bacteria have a double structure that is thinner with less peptidoglycan and more attachments on the outside instead. Gram staining is a quick identifier for different groups of bacteria and typically these groups of bacteria have different susceptibilities and other characteristics. For example, many gram positive bacteria are involved in cellulose degradation in the rumen and many starch digesters are gram negative. Pathogens such as Escherichia coli O157:H7 and Salmonella are also gram negative. So gram staining is a tool, and our professor wanted to show students how it was done to refresh their memory.

So we used this video?

Awkward moment in class and I'm not sure how that was a good use of our time. This professor is really good at using powerpoint as a tool instead of a crutch. Great images and limited text, but sometimes his cartoons and video choices just make me scratch my head... I think that back when I was in undergrad I didn't value my time as much as I do now, but all I could think when we were in class that day was "Why can't we just get out early instead of watching this so I can get back to my proposal?"

Week 72 - Bearded

Twas the week after Christmas (Dec. 29 - Jan. 4) and all through the house

Were gifts still wrapped and a very happy mouse

The cold weather had driven the rodents all in

And daddy had to remove them again.

Hannah was opening yet more gift

The box full of blocks and the paper was ripped

But one rip or two, she still couldn't quite see

So Dad and Mom helped to expose what's beneath

Blocks are so fun, can't you see?

Towers and tunnels and houses for me

And when it's all built, I swipe right on through

With my hand or my foot, to start building anew.

"Who me? I couldn't have knocked down the tower. It must've been Mommy."

I'm not much of a poet, but since we got that book for Hannah this year, it seemed fun to parody it for just a minute. Hannah's Christmas continued and this week she moved on to a new solid food - celery. Celery seems to be a great thing for her as she has two teeth to catch the fiber a bit and the body of the celery give her something to bite down on with her gums. Our daughter is such a healthy little girl.

One of the little blessings this Christmas has been how much some of our family has bought into Hannah's education fund. Yes, education is really important to us both and we indicated early on that more practical use of money gifts towards her education fund would be something she would appreciate down the road when she was older. I know in our family that she will learn the value of education and be very thankful for this support. And I am grateful to our family for being practical and loving -giving a gift like that isn't always exciting, but it's not gifts that are exciting that always matter. We aren't saving a lot, but it will add up over time and this is a gift that means a difference for Hannah's future.


This week is nearly all relaxing or visiting with family. I've been messing with gadgets, cleaning up spots in the basement and just trying to get some extra reading done in my spare time. Not much going on at work. In fact, the only other big news is that I am settling into my winter beard quite comfortably. I finally had to trim it up a bit and tame down the wild man, but my wife doesn't hate it entirely. In fact, I shaved it all off once back at Thanksgiving and she told me didn't care. So the new plan is to let it grow up a bit. Hannah seems to like grabbing at it and my face keeps a bit warmer in this cold. It has been so blasted cold lately. We already cancelled the beginning of classes and closed the university due to the cold and it doesn't look to let up soon. The only warmth this week came from the Spartans at the Rose Bowl. Finally, finally, finally! What a great triumph for a team that knows the meaning of struggles and failure. Victory tastes so much sweeter when you can still remember the feeling of defeat.

Week 71 - Autofocus

This week is Christmas, and as such, about time for me to admit I'm fighting some bugs. Having Hannah in daycare brings home just about everything and when she isn't sniffling, my wife is running a fever, and when they both feel fine it's my turn. So we've all passed bugs around and with any luck that's the end of it. Someone heard I was feeling a bit down this week and shared a photo with me. I may not be a doctor yet, but I'm pretty sure this would be the perfect prescription for most any ailment. After all, when has more whiskey been a bad thing? Well... there was that one time... let's just say I've learned a few lessons along the way.

Figure out if the girl you just met has a boyfriend, or two.

Note, don't mix with heavy doses of NSAIDs...

Don't leave anyone behind when you bike home...

Get a better picture of the concert of a lifetime with Eric Church...

Never karaoke. Never.

Seemed like a good idea at the time... doesn't mean it was.

Not as cool as you thought you were...

Pay for a hotel room. Your neck will hurt in the morning.

Watch out for curbs.

Don't forget the girl passed out in the bathroom.

Things might be louder than you expected.

Let your friends cut you off if you forget to do it yourself.

Biking with 60 beers is hard enough, do it sober.

No 2 people should ever be served this much at once. Not even if they are champions.

Anyhow, so it's Christmas this week and we are very excited to celebrate it as a family. With the LOI out of the way and a break between period 3 and period 4 of CO35 (our advisors both banned fermenter work over Christmas break), we have a bit of time to sit and relax as a family. It's cold here now, thought not too cold, and fires in our fireplace are much nicer this year with dry wood. Last year's green/wet stuff was not really that fun but now we have some real fires. Christmas day, that's where I sat the entire morning and afternoon. I love to feel the warmth on my back.

The in-laws came over to visit and we all crowded back into the fireplace room, pretty much a miracle. Hannah didn't really figure out the whole gift opening thing, so there are still a few gifts down there that will probably be waiting for a few weeks. She would much rather just chew on the bows, so helping wrap gifts the week leading up to Christmas was just as exciting for her as the gift-opening festivities afterwards. We have also made it one year into the Santa Claus gig, and I am actually in full support of it. My wife talked me into it and I have to admit that my take on it has changed a bit. I suppose it is good for a child to have something to believe in that's exciting, to perceive the world as magical and happy. We all know that once they grow up and realize what a twisted piece of crap we've turned it in to, they'll wish they could just go back to believing in Santa again. 

Who needs gifts when you can soothe your gums on a bottle?

I would be remiss if I didn't say thank you to everyone for the thoughtful gifts this year. I feel very special and loved, and I would even if I didn't receive anything. But the thought that went into the gifts means a lot to me.

The holidays are also airsofting season around our house, so I thought I would share a couple pictures of the top tacticians in the game, still living high after the night ops ambush back in October. Don't ask me why but we always seem to airsoft when it is literally freezing cold outside. I think it has something to do with better turnout when people have more layers to stop the pellets. Whatever it is, tactics go out the window for my sister once she has to sit in one spot where her hands on a cold, metal trigger. So let's just say she didn't fare as well this time as we did on our last trip out. Guns also seem to jam a lot and while some people have an intuition for a bad gun or jammed magazine, she doesn't. I caught up to her once only to find out she had been firing blank for over 30 minutes. I want to help so badly but I just don't know where to start...

Sis in her show-off pose before she realized she didn't know how to use the gun.

With all of the Christmas gifts and time spent at the parentals', I went in search of my old camera case so that we might be able to use it for our new camera and the extra lens that we bought with it. In the process, I dug out my old point and shoot by Olympus. Twenty years ago, this was as good as it got in the automatic camera world, complete with a digital display on top that told you how many pictures were left on the roll of film! We sure have come a long way since then, but sometimes I think the technology now supersedes the ability of the people who possess it. Back then, we had to struggle to get autofocus to pick up on the right things; it was touchy and unpredictable. But with practice, we figured out how to train the focus on different parts of the frame to change the light reading and exposure even though the camera didn't come with any settings to choose from. People marvel now at the pictures I can take with a digital point and shoot, but you have to realize where I came from to understand why I can get such great performance out of simple cameras. With all of the settings that are available now on the cameras, how could you go wrong? There is truly a setting for anyone's preferences. But people just plan on the camera to correct everything for them and can't figure out why their pictures might not be as good as they hoped.

The things is, we have so much technology now that we take for granted it will make our lives easy, and it does. But in the process of making our ability to take pictures easier, we have dumbed down the art in the process. And that is just like statistics in my everyday work. Graduate students and even professors have this mindset of autofocus - we will run stats the same way everyone else did before us and report the data just like that. But without knowing experimental design and the correct way to analyze data based on the specific experiment in question, scientists are not using the full scope of new stats programming to their benefit. They lose accuracy, power and ultimately impact from their data either by analyzing incorrectly and counting on the program to make corrections or by under-analyzing and not using their brain to determine what should be modeled and examined. It is a challenge even for me up on my soapbox to remember not to just "plug and chug" with statistics but to be thoughtful about what I look at and why I do it. We need to look past the autofocus and remember how it works and what it can do for us.

Week 70 - Manganese

This past week (written for December 15-21), my cousin tagged me in a post on Facebook, telling me how tolerant I used to be of their shenanigans and whatnot. I thought I would throw the photo in here as proof - I was nice, once upon a time. You can see him laying backwards in the right hand side of the picture, and the youngest one sitting on my back. For some reason I was just a jungle gym to them, and all they wanted for their birthday every year was for my and my siblings to spend the night and hang out with all four of them. What a crew it was, 7 of us tearing around the house. I always hoped I would be a good example for them, unfortunately, one of them passed away suddenly from a stroke when I was a freshman in college. She is missed all the time, but at least I know that she has company up above.

As we wrapped up period 3 of CO35 this week, I had a sudden thought while I was taking out my contacts at home. The "aha" moment was precipitated by my very aggressive contact solution I have to use to keep my eyes healthy. In the old days, I could go for days, even over a week without taking out my 2-week contact lenses, and rub them full of dirt and smoke from camping without being bothered at all. But as time passed, and they were beat up more often - sunscreen/sand in the grand canyon, dust from the dairy farm feeding job, whatever I brought back from Mexico... - my eyes would burn with the slightest provocation. It got to the point where I finally had to go to the doctor and he recommended weeks of no contacts and no exposure to dust. Of course, living in Michigan in the summer, this meant time off from work and spent inside only - boring. But the other option was eventually not being able to wear contacts ever again, or being blind. Knowing there are many people who would give anything to be able to see, I had to do what I could to save my eyes. This included upgrading to a more expensive eye care solution. I agonized about the price, and the amount of solution I had to use to refresh the contacts every night, but after even a few weeks I could feel a huge difference in my eyes. Yes, folks, this is my open endorsement of Clear Care as the reason I enjoy wearing my contacts again. My eyes have been healthier, my scar tissue has healed and I am so much happier.

The science behind the product is pretty cool, too. Basically, the little stubby piece at the bottom is manganese oxide, and this serves as a catalyst to convert hydrogen peroxide in the solution to water in 6 hours. The hydrogen peroxide sterilizes your lenses, killing bacteria and the water is there in the morning. Well, since manganese oxide is oxidized and available to pick up hydrogen, it got me thinking that maybe if we could just increase the manganese fed in animal diets, the cost would be minimal but the alternative source for hydrogen sinking would not be toxic or have other side effects like so many of the methane mitigation strategies proposed. I searched briefly through the literature for a day and learned that we really have no idea about manganese in the animal diet, except that it's important. We have certainly not tested it as an option for methane competition. Unfortunately, I don't think it will work that well because it is not as thermodynamically competitive for H2 as other compounds, so less punch for the money. But since I have a lot of manganese laying around, I thought I would test it out at work anyhow. I've heard from the interns before that I make science seem a bit more fun than they would have imagined, and that makes me feel a bit proud inside. So when we toss around ideas like that and I just say, "Well, we can test it", everyone gets a bit excited about it.

I wanted to know how much manganese might be consumed in a day by the microbes, and if the manganese could be toxic to them as well. So I had to first remove the piece from an old contact case, then weigh it and find a method to attach it where it would not spin around in the fermenters and eventually lodge under the magnet, destroying the fermenter jar. Random experiments are great when they don't destroy equipment. So I used a rubberband and attached it to a metal rod, then stuck the metal rod through a drilled out rubber stopper. Voila! The manganese could be dosed and I could see control vs. responses to the manganese in different fermenters. I fed them and waited until the next day. Unfortunately, there was no difference in methane production, which is good because it means that I didn't have toxic enough manganese levels, but I am betting that the surface area of the solid vs a powder has a different response, because the effective dose would be changed. This isn't really the main area of my research, but if there is anyone out there interested in taking the idea further, you can thank me later. It is possible the idea could work, but I don't think so because you would have to dose this every day to mitigate methane and either feed very high concentrations of manganese or manually dose the animal. The bolus idea as I tried was the only one with cost-effective potential because you could dose once with a known quantity of days where manganese would be present. Oh well, just another fun day in the lab.

Hannah discovered the musical snowglobe my parents gave me when I was in middle school.

Home front news is gonna be pretty short today, but all you need to know is that Hannah and Betsy are becoming better friends. I think it is still too early for Betsy to view Hannah as a food source but I think she has just become more comfortable with all the random noises and movements, and accepted that Hannah will be a more permanent member of the family. We are so blessed to have a dog so patient with Hannah, we always joked that we had baby-proofed the dog back when I chased her around on the floor and pulled her ears at all hours of the night, but maybe that really did help. All I know is she is so great with Hannah and when I hear about people having to get rid of their pet because of compatibility issues, I feel bad for them and am grateful we have such a keeper. Adopting Betsy from the shelter wasn't just good for her; she was a great thing for us.

Week 69 - LOI

It never gets old... every time that I look at the abbreviation "LOI" in communications back and forth for my grant, I feel like someone thought something was really funny and then bailed out at the end. But in the grant world, LOI stands for "Letter of Intent". So what is a letter of intent, and why did it absorb so much of my week?

Well, the letter of intent is designed alert a funding agency that you intent to apply for their grants. In many cases, the number of applicants is so vast that the letter also helps sort out some of the applications that will definitely not make the cut either due to poor fit for the request for applications (called an RFA) or because they are not of the caliber or lack the potential to make the final cut. So in two short pages you are expected to tell people who know nothing about your field of work what you will research and how it relates to their funding. It took nearly all week, with normal work in the lab mixed in, of course, to get all the words fit into 2 pages without sacrificing line spacing or font size. So now it is turned in, and I have received confirmation it was received. The next trick is that I have to get my candidacy exams done before February 20th in order to qualify for this fellowship grant. That means in just 2 months, I need to prove that I know enough about dairy nutrition, general nutrition concepts and methane production to deserve consideration for a doctorate. So much for relaxing over Christmas...

Something that has been proving to aid in relaxation is the new bourbon barrel lager. "Home run" fails to adequately describe how well this turned out. So to Colin, thank you very much for loaning me the use of your barrel, this would have made you proud and I am saving a bottle for both you and your lovely wife. Just smelling the beer warms my heart on a winter evening, and it serves great at cellar temperature - bringing out the subtleties of the bourbon. Four months from start to finish, this beer was worth the wait and we will be making a new batch soon. In the meantine, I've put another fifth of whiskey into the barrel to keep the wood happy. The debate now is whether there should be a chocolate bourbon or a cherry bourbon. Too much cherry is a bit more of a risk than failing to capture the soft flavor of chocolate amidst the fermentation.

Once I am rich and famous, I think it would be fun to run a place like the cellar we visited this weekend for a wedding. Stocked with wine and tucking away cold molds with the drippy water, this felt cozy and classic. I tried to capture a panorama to give the idea of how the cellar extended off in different directions and levels, but it doesn't really do the place justice.

Panorama of our cellar-bar wedding this week.

My week has obviously been entirely absorbed by this letter, evident from the lack of photos in my phone this week. Hannah is nearing 6 months old and her interest in Betsy is renewed. Betsy is warming up to her, too, acting more comfortable around her just so long as it doesn't come at the expense of her food or toys.

This week Hannah really enjoyed watching Betsy eat.

I will leave you with just one more thought. A band friend of my wife's shared this with me in good fun after I saw him last week during their loss to MSU. All the email said was "Go Sparty", and I have to agree. If you earn the right to represent your conference, it is your obligation to make good on that and bring home a trophy for the conference. Two great teams clashed and only one could go to Pasadena. Now we have to prove it was the right one. I hope this week that the boys in EL are relaxing before their bowl practices and preparing mentally for one of the greatest games in MSU history. Go Sparty!