Archive for December, 2011

First Life

31 December, 2011

 First Life: Discovering the Connections between Stars, Cells, and How Life Began 

by David Deamer, PhD

What a wonderful book, just published this year. I sincerely wish that someone had given it to me when I was taking first year chemistry and biology years ago.  Deamer explains how how simple chemical reactions lead to important parts of cell biology. He writes the story of scientist trying to figure out how life first occurred in the sterile environment of a lifeless earth. He writes with humility and honesty about the scientific process. He openly and often points out the challenges in understand that scientist do not yet understand.

So, here’s how I found the book. I decided to read/work through…I dunno, maybe learn…Cell Biology, using an old classic text. Of course they start with a chapter on Origins of the Cell.  I wanted some background reading, because for me, I like lay summary before I get into the details so I can see the big picture.  I saw that Cold Spring Harbor recently put out a collection of papers/essays/review-articles about the origins of life. I tried to read a couple…but, next to that collection I saw First Life. On a whim, I picked it up. Very glad I did. My only “regret”, is that previously I had made the decision to ignore astronomy in my personal studies of biology. Now, I see that I need to learn more about astronomy too. So much to learn, so little time.

Questions to answer

  • How was phosphate first involved in life?
  • How did metabolic systems originate?
  • How did systems spontaneously arise?
  • What were first polymers of life?
  • How did the first polymeric catalysts appear?
  • How did base sequences in nucleic acids begin to code for amino acid sequences in proteins?
  • How did ribosomes emerge as molecular machines?
  • The origins of chirality in biology.

One thing that was clarified for me, all chemical reactions are reversible.

And of course, a tid-bit of trivia that makes me grumpy,

One Flew Over the Cuckoo’s Nest

31 December, 2011

I liked it.

Four stars.

Nice flow of dialogue, nice characters, asks big questions (freedom -vs- safety/authority), yet tells a simple story, nicely crafted. Back used only to push current story forward. There isn’t a lot of hack-psychology figuring out the motivations of the characters, even though the scene is mental hospital.

favorite quotes:

“As my sociology professor used to emphasize, ‘There is generally one person in every situation you must never under-estimate the power of.'”

“But it’s the truth even if it didn’t happen.”

And the most beautiful sentence I’ve read in a while, “The swells slid by, deep emerald on one side, chrome on the other.”

I wonder if I’ll watch the movie.

MsSqueaky quotes

22 December, 2011

This morning, MsSqueaky said whilst we were driving to school on a very frosty day, “Papa, there’s snow on the cars. It’s not really snow, it’s ice. But I call it snow.”

Yesterday morning, when MyBetterHalf was driving to work, as she normally does, she stopped the car in front of our house, rolled down the window, and waved. MsSqueaky & I waved back, and blew kisses. MrCuddles didn’t want to wave then. And then MyBetterHalf drove on. A moment later, MrCuddles wailed, “I didn’t say ‘bye’ to Mommy!”   I tried to explain, that when he gave her a bye-kiss, that was a way to say ‘bye’. He didn’t stop his lament. MsSqueaky said to him, “Maaaayyy-beeee, when we go outside to go to school, then you can say “bye” really, really loud and she will hear you.”  MrCuddles liked that idea, and quit crying.

Overnight at Church

17 December, 2011

So…the youth were putting on a X-mas pageant. I was there to be-a-gopher, help-out, make-sure-nothing-caught-on-fire for a couple of the new rehearsals.

But let me digress. My awesome friend, Chava, is a youth music director at her church down in Cali. (And yes, every time I say “Cali” I think of LL Cool Jay’s work of genius. Don’t you?  “…I don’t think so”) So her kids, and ours were both performing Angels Aware! (BTW…I do like the song “The Perfect 10” and hope to learn it on guitar to sing with my childrens.) Wait, was there a point to this… oh yeah. She had to cut one of her stars because they couldn’t make the performances, by-the-way. Imagine telling your sports coach, “I can’t make the big game, but can we still do all the practices with me as the star.” You’ld be running laps. I mentioned this story to some of the adults in charge of the performance up here. And one of the older teens heard it, and he thought it was a brilliant idea, and wanted to make other kids run laps when they weren’t paying attention. Oh, sigh.

So, Friday the 9th, was the overnight for the youth, 4th grade through high school.

I showed up at the end of dinner. I went into the side room where the adults had sequestered themselves from kids. “We’re hiding,” they said. I showed the things I brought I thought would be useful, a large Maglite and Oreos. They commanded me to hide the cookies.

We ate pizza.

They went on stage for dress rehearsal. I watched from the pews.

Then, after 10pm, was play time. I played pool, table tennis, catch, …and eventually, when the church building was all ours, we played hide-n-seek. Lemme just say, teens are so easy compared to pre-schoolers. I didn’t have to worry about them eating anything dangerous. (Like for instance, one of my 5 year old nephews…he ate a X-mas light bulb. Don’t worry, he was alright.)

When time for calm down, I pulled out the iPad, and played a Sesame Street video about the number 7. The teenage boys all gathered around, and quietly watched.

Bedtime by 2AM.

The whole event, for me, was fun and relaxing.

(Side note… so many flashback for me, the adult/director getting more nervous and stressed…the kids paying less attention. Then, five minutes before the performance, a quick “you guys are gonna do great” speech from the director. More than half of my professional teacher/conductors would do that. )

The performance Sunday. Went fine. The thing I was worried about, transitions and microphones was alright. Before it started, my childrens were in the balcony. MsSqueaky saw her friend Katie dressed like and angel, and she wanted to go down stairs and be an angel next to the stage. Katie, saw all her friends in the balcony, and wanted to go up there. Eventually, I got my childrens in angel robes, next to the stage, but they didn’t stand in front of everyone. Maybe next year, they’ll have less stage fright.

NBA 2011

16 December, 2011

OK…so, this post has been a long time coming, because for some unknown reason it is important to me, I feel strongly about it, and I want it to be perfect. Well…that ain’t gonna happen, so I best just put pixels to screen and years later, I can read about how insane I was being emotionally invested in a sport that I can not play.

First, the NBA needs villains. Summer of 2010, Lebron James did a good job at becoming a villain in his inept handling of leaving Cleveland. Now, I do admire that he said, “I want to win” and he took a pay cut. Unlike, say A-Rod. I really don’t have a problem with these freaks of nature getting multi-millions to play a game, because there are billions made off of their entertaining us, and it’s only right that they get a portion of the riches. But back to villains, I was a bit disappointed in the whole Miami Heat team during game six of the 2011 NBA finals. Last five minutes, all the sudden Dallas is pulling down offensive rebounds, which is something Dallas could hardly do the entire series. It seems that the Heat, collectively, gave up. Villains don’t give up. That’s not the way the narrative is supposed to work.

Second, during the lock out, I was totally in favor of the players. I’ll break it down bullet point, since, well…I’m lazy.

  • People buy tickets to see the players.
  • Owners do what? Most don’t even own the building their team plays in. Often, when they are losing money, they will blame the facilities, and ask the city to build them a new arena.
  • 57% BRI… if income is less than the salary, then the players got less income. Players could only get 57% of income, no matter what their salary was.
  • The players, the product… are not easily replaced. These guys are one-in-ten-million talents.
  • As Malcom Gladwell so eloquently said, “Pro sports teams are a lot like works of art.”  It’s not about making money, it’s about owning something really cool, and really rare.
  • The whole Seattle Sonics fiasco, where Mr-Starbucks-Coffee, who taught the world to buy a $4 cup of mediocre coffee, says, “I’m losing money” five years after he promised Seattle “we’ll be champions in five years”. And what does he do, sells the Sonics, and pockets tens of millions of profits, even after yearly losses. No wonder he’s a billionaire.
  • The OKC Thunder…you know, the team that used to be in Seattle…they’re doing great, they have smart management, they’re in a small market and they can compete, they have a low payroll. What we could have had!!
  • During the lockout, what were the players doing? They were connecting with fans, playing charity games, getting the NBA-entertainment product out and building the NBA brand, all while not being paid by the NBA. I’m really impressed with how few idiotic statements the players made during the lockout.
  • Owners claimed, “we losing money”. Players Union said, “show us the books.” Owners never showed the books.

Of all the lockout issues, the only one I cared about was the BRI. I honestly believe the players should have 57% of basketball related revenue. I don’t care about length of contract. I don’t care about salary caps. I don’t care about luxury tax.

Well, it does feel a bit cathartic to get this off my chest.

I guess I should now get around to watching those dozen games from 2011 playoffs that are on the DVR…  Srsly, I still don’t know how Dallas got past LA.

proud of my childrens

12 December, 2011

Over the past few days, my beautiful childrens have given me little examples of things that make me smile.

MrCuddles, has been pushing a baby in a stroller around the house. Sometimes with his sister, sometimes on his own. He’ll stop and talk to the baby, he’ll announce to the parents where he’s taking the baby, (“work” and “park” are popular), and sometimes, he’ll bring his baby up to me, and softly say, “Do you wanna hold her papa? It’s Shar-nee.”

MrGrunty, the other day I gave him some multiple-choice scratch sheets. He was very excited when he scratched off a box, and then found a star. Then I told him how to read the rows and columns, and he liked that. He would then yell when he found a star, “At Two B”.  (Ah, already reading cartesian points…I know, parents are crazy.)

MsSqueaky, she brings her little HotWheels pink Cadillac to me, and tells me “Here papa, you can have it.”  I say, but sweetie,  it’s yours. “You can keep it because you like it.”   And I know that meant a lot, because the other day, she freaked out when we couldn’t find it for her to take to school.


11 December, 2011

Tonight, the childrens and I went caroling with the McCombs. We did a few of their neighbors, and then AkiJamesEdgarDave and then we went to Jenn&Finn.

The childrens were too shy to sing.
MrCuddles fell down some steps, and got a bloody nose. Don’t worry, he was acting normal, and still wide awake at 10pm.

a bit of history on government funding of science

4 December, 2011

Terance Kealey, PhD, has claimed that historically governments did not fund scientific research. Dr Kealey is a biochemist, and so can be excused from not knowing his history. Allow me to help.

He said, in a March 3, 2003, Scientific American interview: ”  The British government only started to fund science because of the Great War [World War I].” and  “Until 1940 it was American government policy not to fund science.” Both of those statements are false.

The British goverment, before WWI funded:

  • Shakleton’s Trans-Antarctic Expedition
  • Royal Society (1850, 1000pound grant-in-aid, increased to 4000 pounds in 1876)
  • The Longitude Act of 1714 – set up a prize by UK parliament.
  • the Toronto Magnetic and Meteorological Observatory constructed in 1840

The American Government also funded science before WWII

The USGS -from River Science at the USGS (2007)

  • pg 17 – (1894) “Congress appropriated funds to the USGS for ‘gauging the streams and determining the water supply of the United States’ (U.S. Statues at Large, V. 28, p. 398).
  • pg 67 – G.K. Gilbert (1914 and 1917) “study of the movement and impacts of sediment in river systems draining hydraulically mined sediment areas in the Sierra Nevada (1914, 1917), which, primarily focused on hydraulics, might be called the world’s first environmental impact assessment.”
  • pg 17 – (1933) Tennessee Valley Authority “to build dams to control floods, improve navigation, provide hydroelectric power, and to develop programs for soil erosion control and reforestation for the rural Southeast.”
  • pg 58 – first USGS streamgaging station (1889) on Rio Grande, near Embudo, New Mexico
  • pg 63-64, The Cooperative Water Program (1895) “The three components of the program are data collection, interpretive studies, and national synthesis.”

National Weather Bureau

“The National Weather Bureau Organic Act of 1890 (U.S. Code title 15, section 311) mandates that the National Weather Service is the responsible agent for “***the forecasting of weather, the issue of storm warnings, the display of weather and flood signals for the benefit of agriculture***.” The NWS uses many sources of data when developing its flood forecasts. The U.S. Geological Survey (USGS) is the principal source of data on river depth and flow.”

Other nations/states/governments also supported scientific research:


There is a wonderful book, Science, Medicine, and the State in Germany: the Case of Baden, 1815-1871 by historian Arleen Marcia Tuchman.   Which focuses on the German state of Baden (before Germany was united), and explicitly shows that the funding of science was a priority of the government, which they supported with cash. A few excerpts:

  • Table 5.1 State Expenditure for Science Education  (pg 104) shows that from 1831-1871, every bienium an increase in science education spending, starting 41,240 gulden in 1831/1832, to 415,676 gulden in 1870/1871.
  • pg 167-168,  during the 1850s, “In Baden, the government actively sought professors capable of directing research laboratories where students would be introduced to the methods of exact scientific investigation. Bunsen, Kirchhoff and Helmholtz were all hired for this reason. The government did not, however, limit its support of the experimental sciences to faculty appointments; it also set out immediately to construct research laboratories where these professors would not only conduct their own research but would also teach their students how to apply the exact method of investigation to the study of nature, health, and disease.”

Other German states at the same time (ibid)

  • pg 107-108,  the German state of Saxony in the 1860s constructed new teaching and research labs at U. of Leipzig.
  • pg 174 , “Barvaria, morever, escalated its support, spending one million gulden alone on the Munich polytechnical institute.”  (1850s and 1860s)
  • pg 176…: “unprecedented expansion of scientific and medical institutes in Prussia during the period when Friedrich Althoff headed the Higher Education Section of the Prussian Culture Ministry (1882-1907)….Althoff alone was responsible for the creation at the nine Prussian universities of eighty-six institutes, laboratories, and clinics in the medical sciences, and seventy-seven institutes and seminars in the philosophical faculties, where the natural sciences had their home.” :


  • The Academie des Sciences, “first meeting on Dec 22, 1666…It’s members received pensions from the King as well as financial assistance with their researches.”  (pg 64) A history of science, technology, and philosophy in the 16th & 17th centuries / by A. Wolf (1950)
  • Parmentier, a French pharmacist during The Seven Years War, and a huge fan of the potato was supported by Louis XV (1770) who “gave him a sinecure that let him write and research”.  By Louis XVI, who endorsed an experimental field for potatoes. And by Napoleon, who “financed several projects including factory to process sugar from beets”.   Larry Zuckerman’s The Potato, pgs 82-85.


  • from 1687-1703,  “79 paintings, known as tangkas, which were intended to illustrate a comprehensive four-volume medical treatise called the Blue Beryl…. The paintings were commissioned by the fifth Dalai Lama’s regent, Desi Sangye G tyatso, who stepped in as interim ruler of Tibet…”     pg 76, The Scientist, April 2011.

I could mention…but I only Wikipedia these…

  • Jang Yeong-sil, Korea, circa 1450, scientist selected to serve the king
  • Maragheh Observatory built by Hulag Khan in 1259, Persia
  • the Saint Petersburge Acadamey of Sciences (founded 1724) which support Euler, Goldbach, Bernoulli, and other scientists
  • The King of Spain, founding School of Mines in Mexico (1792), where Andres Manuel de Rio discovered Vanadium in 1801.
  • the National Museum of Brazil (1818)

I am completely in favor of an informed, civil dialouge on the purpose or usefulness of goverment funding of science. However, first, we must acknowledge that this is not trend in started by the United States of America government, but rather a continuing trend of rulers to want to know more about the world.


3 December, 2011

This morning, I went to church to “just be there” in case they needed an extra hand for practicing for the children’s X-mas pageant. I did get to fill in and do the puppet part for Isiah. Watching the bigger kids amused, frightened and reminded me how it used to be. One kid was getting frustrated at mispronounciations. One kid, when scolded, delivered his lines the next few times w/o emotion (I remember doing that). Kids were just interrupting their parents when parent was trying to give instruction to others…one of my favorite responses, in a hushed-yell that mothers are great at “I will buy more donuts!” One of the high school kids was talking taxation, from a left wing point of view, and so I played Devil’s Advocate.

I’m still trying to learn these people’s names, which is bad, I know. Maybe if they played in the NBA I could remember them better.

When I got home, we all went off to a friend’s house for her party. I played monopoly with a couple of second graders…which, had them fighting less. We made some scandinavian potato pancake thing. I had fun cooking them.

Then, we bought our x-mas tree. Mostly decorated by MyBetterHalf and MsSqueaky & MrGrunty. (I did make dinner, do dishes and hang the lights.) After, we decorated/baked more cookies, did the Jesse-Tree, and Advent calendar.


  • MsSqueaky, gasping with happiness when we plugged the lights on for the tree.
  • MrGrunty, practically demanding I hang lights by the ceiling, reminding me of a few years ago, before he could talk, he would shuffle out when he woke up, and point to the lights if they were off.
  • MrCuddles, so surprised at the new shape of chocolate in the Advent calendar. And then throwing a fit when we wouldn’t let him have any more.

After everyone went to sleep, I happened to find a new cat toy and played with the kitties.


Dec 1st

2 December, 2011

Last night, MyBetterHalf had to stay late at work. The childrens were very excited that it was me picking them up, so excited that they couldn’t get ready to go, but were busy running around, hugging me, yelling “Papa’s here!”, dancing, and playing.  We went to the store, and the usual cart for kids wasn’t there. We almost had meltdowns, but I crouched down, and whispered to MrCuddles & MsSqueaky, “You guys are how old? and next year you are going to kindergarten, so I need you to be helpful, and right now being helpful is not crying. If you can do that, we can do something fun after dinner.”

After dinner, we decorated cookies. MsSqueaky picked pink sprinkles, MrGrunty picked blue sprinkles, (which was funny, because just the night before I told them a story about  that I was making up while telling it about those colors of sprinkles), MrCuddles got multi-coloured star sprinkles. As usual, MrG was very meticulus, and was placing each sprinkle individually. MsS tried to make smiley faces. MrC just ate most of his sprinkles.

Then, we are doing the “Joseph Tree” and the childrens each coloured their own little stump, symbolizing the root of Jesse. MsS asked, “Papa, can I color it how I want?” I told her it was hers, and she could color any way she wanted. So she used dark blue, and black, and you can’t see the picture.

After that, “Mommy’s home!” and they ran and hugged her and jabbered about the cookies.

Then, we showed them their advent calendars. They were very excited about chocolate. MrCuddles didn’t like it when we only let him have one.