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It Is Sandpaper

In other words, it is "rough". Here is a basic rundown:

Thursday, the day was horridly busy at work, and I had several late afternoon meetings I had to attend. One in particular was to get nominated again for a standing committee about curriculum. The lateness of my departure from the U frazzled my schedule for the rest of the evening and so began my foray into "chaos".

Friday, I worked in my back office most of the morning, trying to get caught up on teaching plans and research issues I had been lax in during the week. At the end of the afternoon, I decided to go and talk and share libations with my father-in-law. I still felt chaos.

Saturday, I began to realize that I had been having a fair amount of emotional pain due to certain thoughts about my mother's passing. I suspect it may be the time of year, for this was the time of the year in 2007 when my worry for her became larger and larger. It is difficult to believe it has been less than two years that she has been gone. Her birthday, which would be her 81st will be on the 7th of next month. Two years ago she was pretty much house bound because of the cold weather and due to her having had such a horribly long hospital stay that had weakened her. I have been thinking about how deeply I miss her and how I wish I had been able to fix what was wrong. And, I wish I could have her know how much I love her. I think my awareness of my pain about my mother's death had been building during much of the past week.

We did go with a lot of the family to see ice sculptures on display in a nearby village.

Sunday, chaotic feelings continued. The normal routine we have adopted was shot in the foot by activities that had to be attended. Although the day ended on a good note, I still felt shabby and sad.

Monday, I forgot to throw my exercise clothes in the dryer the night before, and could not therefore go walking at my usual time. My clothes are extensive... long underwear shirt, two t-shirts, sweatshirt, three hats, long underwear pants, two pair of sweat pants, winter coat, gloves, boots. With them being wet, I could not walk at my normal morning time. This threw my schedule out of alignment today and added to the last several stressful days. I then had to rearrange my time and my goals to try to find a way to exercise (take my walk) after work. Instead of it being fun and enjoyable, it felt like work when I finally set out for my five miles around 4:30pm.

I went to orchestra practice in the evening. It was nice, but did not relieve stress and/or anxiety like it typically does. I still feel (felt) edgy and out of sorts.

PipeTobacco

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Day 122, But Meloncholy

I have made it 122 days now of consistent walking. And by and large it has been very good for me. On average, I feel more alert, happier, and have less trouble sleeping.

Yet, for the past couple of days, I have felt quite blue. It is hard to shake. I feel pressured from the time commitments of the new semester and I feel stressed about some financial matters of my mother's estate.

So, happiness is eluding me at the moment.

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I Feel Good (Knock on Wood)

It is very nice to say that I feel very good this morning emotionally. I am hiding away in the back office of my lab and working on MY projects. Emotionally, I feel quite calm, even keeled, and even happy. For me it seems that having a predictable routine is VERY good for my emotional health and psychological makeup.

Other than teaching and my research group meeting today, I am planning to stay tucked away quietly from the pressing questions and needs of others so that I may engage in work that helps me feel accomplished and whole. Tonight, I look forward to a wonderfully classic "American" dinner of macaroni and cheese (I made this, and worked very creatively to make it VERY healthy and low fat (whole wheat & very high fiber pasta, fat-free cheese, humus, fat free sour cream, spices and other ingredients to make the classic powerfully flavorful, creamy, and a very healthy and delicious rendition of the classic). We shall have turkey hot-dogs (I know, a little odd as well, but they taste good and are healthy and feel like a childhood comfort food) smothered in spicy mustard, a huge pile of chopped onions and relish. Of course, we will have a large vegetable with this and a huge salad. It should be grand! Additionally, I look forward to a quiet evening at home with my wife. We likely will watch tv and chat away the evening (or perhaps also have some physical intimacy [furry-faced grin] if I am lucky!).

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Stop the Beast!

This article is excerpted from Science News
from Jan. 17, 2009:

As bacteria resistant to commonly used antibiotics continue to increase in number, scientists keep searching for new sources of drugs. One potential new bactericide has now been found in the tiny freshwater animal Hydra.

The protein identified by Joachim Grötzinger, Thomas Bosch and colleagues at the University of Kiel, hydramacin-1, is unusual (and also clinically valuable) as it shares virtually no similarity with any other known antibacterial proteins except for two antimicrobials found in another ancient animal, the leech.

Hydramacin proved to be extremely effective though; in a series of laboratory experiments, this protein could kill a wide range of both Gram-positive and Gram-negative bacteria, including clinically-isolated drug-resistant strains like Klebsiella oxytoca (a common cause of nosocomial infections). Hydramacin works by sticking to the bacterial surface, promoting the clumping of nearby bacteria, then disrupting the bacterial membrane.

Grötzinger and his team also determined the 3-D shape of hydramacin-1, which revealed that it most closely resembled a superfamily of proteins found in scorpion venom; within this large group, they propose that hydramacin and the two leech proteins are members of a newly designated family called the macins.

The full citation of this published work is:

Jung et al. Hydramacin-1, Structure and Antibacterial Activity of a Protein from the Basal Metazoan Hydra. Journal of Biological Chemistry, 2008; 284 (3): 1896

This discovery is a monumental achievement and I suspect that before 5 years have passed, powerful new, effective treatments for bacterial infections will appear. And it is about time, in my opinion. I think most physicians state the "party line" about antibiotic resistance a bit too much. It is illogical. If you give antibiotics to a patient with NO BACTERIA (which is the physician's argument AGAINST GIVING ANTIBIOTICS), there is really no logical way the claim of "increased antibiotic resistance" can even be made. It is all b*llsh*t. The truth is that antibiotic resistance can and does arise when people DO NOT TAKE THE FULL PERSCRIPTION OF AN ANTIBIOTIC. Pure and simple. It annoys the hell out of me when I run into a physician who tries to bulldoze me with nonsense.

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To Think About

The Readings from Mass this weekend and some of my thoughts:

The lamp of God was not yet extinguished, and Samuel was sleeping in the temple of the LORD where the ark of God was. The LORD called to Samuel, who answered, "Here I am." He ran to Eli and said, "Here I am. You called me." "I did not call you," Eli said. "Go back to sleep." So he went back to sleep. Again the LORD called Samuel, who rose and went to Eli. "Here I am," he said. "You called me." But he answered, "I did not call you, my son. Go back to sleep." At that time Samuel was not familiar with the LORD, because the LORD had not revealed anything to him as yet. The LORD called Samuel again, for the third time. Getting up and going to Eli, he said, "Here I am. You called me." Then Eli understood that the LORD was calling the youth.
So he said to Samuel, "Go to sleep, and if you are called, reply, 'Speak, LORD, for your servant is listening.'" When Samuel went to sleep in his place,
the LORD came and revealed his presence, calling out as before, "Samuel, Samuel!" Samuel answered, "Speak, for your servant is listening."

How can I listen better to the calling of what I should do with my life? I firmly believe the best thing I can do in life is to live my life as one of service to others, but if I self-examine my life, I find that I am horrid, a wretch, and without any merit. Why cannot I be better? Better yet, I should be asking why DONT I work harder and more diligently to be a servant?

Brothers and sisters:
The body is not for immorality, but for the Lord,
and the Lord is for the body;
God raised the Lord and will also raise us by his power.

Do you not know that your bodies are members of Christ?
But whoever is joined to the Lord becomes one Spirit with him.
Avoid immorality.
Every other sin a person commits is outside the body,
but the immoral person sins against his own body.
Do you not know that your body
is a temple of the Holy Spirit within you,
whom you have from God, and that you are not your own?
For you have been purchased at a price.
Therefore glorify God in your body

(sigh) Such a difficult passage.

John was standing with two of his disciples,
and as he watched Jesus walk by, he said,
“Behold, the Lamb of God.”
The two disciples heard what he said and followed Jesus.
Jesus turned and saw them following him and said to them,
“What are you looking for?”
They said to him, “Rabbi” — which translated means Teacher —,
“where are you staying?”
He said to them, “Come, and you will see.”
So they went and saw where Jesus was staying,
and they stayed with him that day.
It was about four in the afternoon.
Andrew, the brother of Simon Peter,
was one of the two who heard John and followed Jesus.
He first found his own brother Simon and told him,
“We have found the Messiah” — which is translated Christ —.
Then he brought him to Jesus.
Jesus looked at him and said,
“You are Simon the son of John; you will be called Cephas” — which is translated Peter.



How can I become a better person? How can I put into action what I think about but do not have the stamina to act upon? How can I make a real difference?

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Hopefully A Good Day!

I am doing all I can to make today a good day, I hope.

1. As this is day 117 in walking, I again looked like the Abominable Snowbeast, with an icy mustache upon my return. I wonder how icy my beard would become if I did not have it covered by the face mask? Temperatures are still hovering in the neighborhood of what I wrote about on Wednesday.

2. I am struggling but working hard to stay "Zen" as the Department Meeting approaches today. I have an Human Research Subject Committee Meeting (HRSC) an hour after the Department Meeting starts so I have an "out" to let me be free of the Department after one hour. It is ironic and somewhat humorous that the HRSC Meeting, which is typically very dry and dull is something I am actually looking forward to attending because it gets me out of the meeting I dread!

3. I have a decent and well defined list of accomplishments I would *like* to accomplish this weekend. They are doable and leave time for play as well. So, hopefully the weekend will be wonderful.

4. I have the option to go "hang out" with my father-in-law this afternoon after all the hellishness of the day is done. Pipes and libations will likely ensue if I do go there which could help reset my mind to a more peaceful arena.

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Still Feeling Stress & Now Dread

Still feeling the stress of the first week as my upper division course has its first laboratory session this week. We have already met for lecture, but the lab portion is truly like an additional course with additional goals and objectives. After I get it under my belt, all should feel better... Except....

We are having our first damn Department Meeting of the Semester this Friday. As much as I try to put it out of my mind, and try to not feel anxiety or stress about it, I hate and despise going to these things. You may recall the meeting we had close to the end of the semester in December where ole Ed acted like an obnoxious idiot and I allowed myself to be upset about it for days. This is not the only time something like this happens specifically in the Department Meeting. It is frustrating because one-on-one I generally like and get along with most everyone in the Department. But in these meetings, some of them just become absolutely egomaniacal and downright rude and hurtful. I have not liked going to Department Meetings for the last five years or so.

I am going to attempt to acquire a "Zen" attitude about it all, but it is awfully damn hard.

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Day 115!

I am happy to say that I have now walked 115 days in a row! AND, all of my friends in warmer climates will be even more surprised to know that we have been experiencing Arctic temperatures. The actual temperature when I walked this morning was -12 degrees Fahrenheit (-25 degrees Celcius) and the wind chill factor made it feel as if it were -42 degrees!. I wore a face mask like this and I came back into the house with inch long (2.54cm) ice sickles hanging from my mustache (the only exposed area so I could breath through my mouth). It was fun!

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Too Damn Busy For Emotions

As it is the first week of the new semester, I am unfortunately too damn stressed and busy to have emotions, so this week it seems a rather moot point. Unless, of course, you count my STRESS as my emotion.

I guess that works. It is how I am feeling. It is aggravating that after these far too many years of teaching that I still feel the stress and anxiety at the start of a semester. Yet, it is comforting to know that at the end of this first week, I will feel back up to snuff and will have smooth sailing (fingers crossed).

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How Cheating Ants Give Themselves Away

From ScienceDaily (Jan. 11, 2009) — In ant society, workers normally give up reproducing themselves to care for their queen's offspring, who are their brothers and sisters. When workers try to cheat and have their own kids in the queen's presence, their peers swiftly attack and physically restrain them from reproducing.

Now, a new study published online on January 8th in Current Biology, explains just how the cheaters get caught red-handed. Experimental evidence shows that chemical hydrocarbons produced by those sneaky sorts are a dead giveaway of their fertility status.

The findings represent the first direct evidence that cuticular hydrocarbons are the informational basis for the ants' reproductive policing, said Jürgen Liebig of Arizona State University.

Earlier studies had suggested that other aspects of reproduction in insect societies are regulated through cuticular hydrocarbon signals. Liebig's team and others showed that the chemical profiles are correlated with fertility in queens and workers in many species of ants, some wasps, and bees. They also found that workers use hydrocarbons to discriminate between eggs laid by workers and queens. The chemicals are used in other contexts as well, including nestmate recognition and sexual attraction.

Given all the evidence that hydrocarbon profiles play important roles in communication, Liebig and colleagues had a strong suspicion that they would also help catch reproductive cheaters.

To test the idea in one ant species (Aphaenogaster cockerelli), Liebig and Adrian Smith, also at Arizona State, mimicked reproductive cheaters by applying a synthetic compound typical of fertile individuals on non-reproductive workers. That treatment attracted nestmate aggression in colonies where a queen was present, they report. As expected, it failed to do so in colonies without a queen where workers had begun to reproduce.

Liebig thinks the cuticular hydrocarbons are an "inherently reliable signal" because the ants can't separate their own hydrocarbons from those of their eggs. Masking their own fertility would mean displaying the chemicals of a worker, but their eggs are best hidden if they seem like those of the queen. But they can't have it both ways, he says.

This system for catching cheaters plays an important role in maintaining harmony in the ant world, Liebig said, and it sets an example that we might learn from ourselves.

" The idea that social harmony is dependent on strict systems to prevent and punish cheating individuals seems to apply to most successful societies," he said.

"Understanding what mechanisms are employed within ant societies, which are perhaps the most successful and widespread among all animals, provides a model for understanding the fundamental basis of successful cooperation."

The researchers include Adrian A. Smith, Arizona State University, Tempe, AZ; Bert Holldober, Arizona State University, Tempe, AZ, Universitat Wurzburg, Wurzburg, Germany; and Jurgen Liebig, Arizona State University, Tempe, AZ.

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It is not surprising to me in the least that endocrine/pheromonal signals will give the "cheaters" away. Endocrine/pheromonal cues are abundant in nature including in humans. The female human, exudes odor cues when she is at the peak of fertility even though we, as humans are not particularly adept at recognizing such.

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Libations Flow In My Veins

As I was feeling out of sorts about the start of the semester, I decided to go quell my sorrows with my father-in-law. I am a bit tipsy, but feel less anxiety.

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Feeling Stress About New Semester

Not much more to say than the title. It is that time of the year where I feel all sorts of irrational stress about starting a new semester. It would be better to skip these next few days and have it simply be Monday.

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108

No, not the temperature, but the number of days today that I have walked EVERY day! Today's walk occurred during a snowstorm and so was quite beautiful and once I was warmed up a bit, the snowflakes falling on my face melted readily and were pleasantly cool. My mustache and beard looked something akin to this fellow when I finally returned home. I am hoping for a wonderful day today and am trying to ignore the upcoming dental appointment and trying to not let people distract me.

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Sadness Due To Being "Tugged"

I am experiencing sadness today that I attribute to having had a day where none of the work I had wanted to do and had planned to was able to be worked on as I was pulled in a myriad of different directions by all sorts of different forces at work.

I left exhausted and sad. Add to this an upcoming dentist appointment I am not looking forward to on Thursday. My new dentist (the prior one retired, sadly) is "trendier" and does not replace fillings with amalgams as was common practice for decades, but instead ONLY uses the white porcelain replacement material... which is brittle. This is fine in many applications, but I have TMJ, and this results in me exerting enormous grinding pressures on my molars even when I wear "bite guards". To make this long story shorter... because I grind my teeth, the idiotic white fillings they put in my molars (to replace the old amalgam they said was "worn") have broken three times now. They are itching to grind out my beautiful tooth and put a crown in instead, which I DO NOT WANT! So, I am girding myself up for a battle on Thursday as my latest filling in this tooth fell out this afternoon.

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Interesting Way To Make Discoveries

The following excerpt outlines a process in science called "Systems Biology" which they are suggesting is crucial to future advances in biomedical research. I agree completely and feel that the effort is one that should be applied to many more tiers and subdisciplines in biology as well. To me, this may be the next breakthrough in HOW to research in biology that follows the monumental breakthrough that Platt's 1964 paper "Strong Inference" had at that time.

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Published on 5 January 2009
by Insciences

Key to future medical breakthroughs is systems biology, say leading European scientists

Crucial breakthroughs in the treatment of many common diseases such as diabetes and Parkinson’s could be achieved by harnessing a powerful scientific approach called systems biology, according to leading scientists from across Europe. In a Science Policy Briefing released today by the European Science Foundation, the scientists provide a detailed strategy for the application of systems biology to medical research over the coming years.

Systems biology is a rapidly advancing field that combines empirical, mathematical and computational techniques to gain understanding of complex biological and physiological phenomena. For example, dozens, or even hundreds, of proteins can be involved in signaling processes that ensure the proper functioning of a cell. If such a signaling network is disturbed in any way, diseases such as cancer and diabetes can result.

Conventional approaches of biology do not have the capacity to unravel these elaborate webs of interactions, which is why drug design often fails. Simply knocking out one target molecule in a biochemical pathway is turning out to be a flawed strategy for drug design, because cells are able to find alternative routes. It is a similar scenario to setting up a roadblock: traffic will grind to a standstill for a short time, but soon motorists will start turning around and using side-roads to get to their destination. Just as the network of roads allows alternative routes to be used, the network of biochemical pathways can enable a disease to by-pass a drug.

Systems biology is now shedding light on these complex phenomena by producing detailed route maps of the subcellular networks. These will make it possible for scientists to develop smarter therapeutic strategies – for example by disrupting two or three key intersections on a biochemical network. This could lead to significant advances in the treatment of disease and help with the shrinking pipeline of pharmaceutical companies using traditional reductionist approaches to drug discovery.

The new policy document, produced by the Life Sciences and Medical Sciences units of the Strasbourg-based European Science Foundation (ESF) calls for a co-ordinated strategy towards systems biology across Europe. The scientists have pinpointed several key disease areas that are ripe for a systems biology approach. These include cancer and diabetes, inflammatory diseases and disorders of the central nervous system.

The report’s authors state that the recommendations outlined in the Science Policy Briefing provide a more specific, practical guide towards achieving major breakthroughs in biomedical systems biology, thereby covering issues that had not been previously addressed in sufficient detail. In particular we identify and outline the necessary steps of promoting the creation of pivotal biomedical systems biology tools and facilitating their translation into crucial therapeutic advances.

The report highlights some recent successes where mathematical modelling has played a key role. The conclusions from these examples are that success was achieved when quantitative data became available; that even simple mathematical models can be of practical use and that the interdisciplinary process leading to the formulation of a model is in itself of intrinsic value.


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I will need to think more and explore more to see if I can find an avenue to apply this thought process to my own research on neuroendocrine function.

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Christmas Sadness

The day is one that feels sad and melancholy, as I am taking down the two Christmas trees and the other various decorations for the holidays. Typically we try to leave them up until January 6th, which is Epiphany, but with today (Sunday) being the 4th, we celebrated Epiphany at mass this week. So instead of waiting until a very hectic Tuesday of this week, we are working on the task today.

It feels sad, not because the holidays are over, but because we are again packing away things that have such memories. Good memories, but also sad ones due to the passing of loved ones.

I will be back later today to catch up on all my comments, so please look there for more from me.

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Spent

Spent the morning at the laundromat washing and bleaching the clothes I had frozen in garbage bags outside. I washed the full set twice.

We had a gathering with my wife's side of the family this afternoon, and while on that side of town, I drove the extra distance and went to mass at the parish I grew up at and my mother was buried from. It left me sad, and I wish I had gone to another parish.

I apologize, I am too spent to write more tonight. I have so much work to do.

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Cockroaches

I am utterly exhausted, so today's essay will be brief. I spent the day traveling several hours to a distant city to help my wife's mentally and physically disabled aunt move up to this region. Unfortunately, where she had been living was in a very low-income tennament that was filled to the brim with insect infestations, especially of cockroaches... literally thousands of them.

We emptied and packed her apartment and made it home, but the mental toll was great due to the worry about bringing back some of those horrid insects back. I changed clothes and shoes in a public restroom after getting out of her apartment and sealed the clothes in a garbage bag. Then at home, I stripped in the garage completely from the second set of clothes and shoes (which also were bagged)and left both bags outside in the sub freezing temperatures to hopefully kill any of the pests. I then went into the house, naked, and showered completely 5 times before coming out.

In the morning, I will take the frozen clothes and shoes and take them to a laundramat and wash them in the hottest water, soap, and bleach the machine will allow and dry them at the highest temperatures the dryers offer.

The highlight of the day was after showing all those many times, I came out and enjoyed my first pipe of the day. It was truly special.

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Quiet, Peaceful Workday

On this, the first day of the year, I have purposefully gone in to work because of the wonderful peace and tranquility of having no one else about in the whole place! I have gotten a tremendous amount of organizing and cleaning done, and have been able to contemplate plans for the upcoming semester that I will likely outline for you as I firm up these plans designed to increase my productivity, my research, my joy, and my fun in life!

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