Over the Dither and Through the Words

The garden plot, finally done

Posted on April 9, 2012 by Ami Chopine

And planted.

I worked every day last week for this. Before I committed, I learned that in the beginning it would take about twenty hours a week. Well, that’s if you aren’t working with an old garden plot that needs to be weeded. I have probably spent about forty hours on this ground. We got a lot out last fall, but not the grasses. I hate grass in my beds.

Three east to west beds terraced above one north to south bed.

After that, time to compost. I had two bags of a compost mix I bought. I spread those on the far south and east beds. I then spread a mix of steer and chicken manure compost (ratio is steer:chicken – 5:2). Continuing to do a bit of yard clean up and making my own compost. But it’s hard. The compost keeps on shrinking. How can I make a 3′ x 3′ pile if it does that?

I’m trying the organic thing. Why organic? Because I believe in biology. I like the ‘first do no harm’ ideal. I think it’s smart to think of my garden soil as a living ecology that I can work with to help the plants. I feel like I’ll be able to grow vegetables that are tastier and healthier.

But I’m scared. I don’t really understand the soil well and not all plants are the same. I’m still at the ‘do what I’m told’ stage, and all the seed and transplants don’t assume organic. That’s a lot for a beginner gardener. Also, watering. In a desert. When, and how much? I’m putting all this work in, and what result will I get?

So, what have I planted so far? On April 7th, I planted carrots with a cardboard box over them so the soil won’t crust over. But went I checked it today, there was quite a bit of drying. Argh. Hope it’s okay this early in the game. I watered again and soaked the cardboard. That same day, I also planted peas (with innoculant), and the sweet onion sets. Today, April 9th, I started the plain onion sets and the green onion seeds. Then I spread the rest of the lettuce. My last lettuce, I kind of treated like weeds. Just scattered them about and left them. No watering or anything. Didn’t do well. These lettuces are on my freshly composted soil with fertilizer and I’ll make sure they get watered.

Two rows of peas, planted 1-2 inches apart. I'm not normally paying so much attention to row spacing, except I'll need a trellis for these. Cardboard in the corner is over the carrots. Hope that works.

I am using a fertilizer. It’s an overall organic one, with lots of micro-nutrients and starters for beneficial soil organisms. So, let’s hope.

Well, my seedlings are doing well, anyway. Their first leaves have shown, and I gave them a bit of fertilizer in my last watering. That isn’t organic. I figure it’s an artificial environment anyway, with the soil sterile. I raised the lights about an inch. Tomorrow I’ll be thinning them all out. I think it may be time to transplant them too.

These are the cherry tomatoes.

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DNA: the molecular goddess

Posted on March 30, 2012 by Ami Chopine

WOOPS! I have two blogs, and accidentally posted this on here. Well, consider this a sample. If you want to see my other blog about this kind of stuff, please visit me at Molecular Me.

In my last post on cell structure, we took a look at cell membranes which are made of a phospholipid bilayer. They protect the cell and cell organelles from the outside environment while letting a few players in and out to do their job. But what is it that membranes protect? Primarily, DNA (short for DeoxyriboNucleic Acid), a molecule that can make copies of itself. How DNA works was the next thing that blew my mind in biology, and pretty much cemented what I wanted to study.

DNA is the ultimate celebrity superstar of molecules. It’s the subject of many a science fiction story, volumes of textbooks and encyclopedias, various t-shirts, jewelry, and a scarf I want to knit someday. Everyone has heard of it, knows what it looks like, and knows that it carries our genes. If DNA is news to you, then you are probably fairly young or you’ve been living under a rock.

So how does this double helix encode our genes? You might think of a gene as that bit of information which gives us our eye color, makes us tall or short, shapes our nose, and gives us ADD (or not). While many of these things can be traced to a single gene, the more accurate definition of a gene is a sequence of DNA which gives instructions to put together a protein.

DNA has an alphabet of four letters, called nucleotides, nucleobases or bases for short. These nucleotides can fit together in two matching pairs called base pairs. The base pairs make up the rungs of the twisted ladder structure of DNA, with the sides being the twinned backbones of the macromolecule. The base pairs connect to each other across the rung, matching molecular shapes in the middle to make a light bond which can be zipped or unzipped. On one side of the ladder is the complementary template, and on the other is the actual code that creates a protein when transcribed.

These four nucleobases of DNA are Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). A pairs up with T, and C pairs up with G. Ever watched the eugenics dystopian movie Gattaca? It’s title refers to the bases of DNA.

Three of these bases together make a word, called a codon. This codon represents an amino acid. The twenty amino acids are the building blocks of proteins. There are also codons which say stop and start. This dictionary of codons which can be translated into amino acids, or stop and start is called the genetic code. How we got this genetic code is one of those mysteries that we still haven’t solved.

When making a protein, DNA is unzipped by certain enzymes, and a copy of it is made. This copy isn’t DNA, but RNA – a single strand instead of a double strand. Instead of Thymine, RNA uses a base called Uracil which still pairs with Adenine. Once the sequence of RNA is copied from the DNA (beginning at the start codons and ending at the stop codons), it is moved to a part of the cell where the protein can be built. This special sequence of RNA is called messenger RNA, or mRNA.

A DNA molecule being unzipped, transcribed, and it's mRNA template going on to a ribosome as a molecular blueprint for building a protein out of amino acids.

Another form of RNA is transfer RNA, or tRNA. tRNA is connected to an amino acid and has an anti-codon which has the three bases matching the codon for the amino acid. The mRNA goes to a ribosome, which is kind of a molecular reader. There can be up to 10 million ribosomes in a single cell. As the mRNA clicks through the ribosome, tRNAs connect to the proper mRNA codon, and then their amino acids are bound together. In this way, the long protein chain is created.

DNA doesn’t just code for proteins. In fact, only about 1.5% of the human genome represents protein sequences. It also has regulatory sequences, which control what proteins are made and how much and structural sequences for the chromosomes. And there can be a lot of repetitive DNA which doesn’t appear to do anything, though we can’t be positive about that right now. All of these can affect our genes and how they’re expressed – in other words, what kind of inborn traits we have. But some of it does appear to be fossils of a type: broken copies of sequences we use or perhaps ones we no longer use. It’s this extra DNA which is another proof that species, including humans, have evolved over time. In the human genome, there are over 3 billion base pairs with approximately 23,000 protein coding genes. We are still exploring what each of those genes do.

So, cell membranes and DNA were the two sirens that pulled me into biology. Before I go any further into the other cool molecules, I think it’s a good idea to get the lay of the land. In my next post on cell structure we’ll take a brief look at a whole animal cell and get a simple description of each of the cell organelles.

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Under the lights

Posted on March 26, 2012 by Ami Chopine

First thing after my workout this morning (2.5 miles run + 20 minutes strength) I came home and put up my grow lights. My setup consisted only of what I had around the house: An unused desk, a couple of extra chairs with good chair backs, an old closet rod, the garage studio fluorescent lighting I mentioned in my last post, and some rope. Rod over chairs, over desk, light strung up using the rope with a slip knot so I can easily pull up the lights. The extra rope is secured so it doesn’t slip. The light is pretty narrow, so I moved my plants within the tray to maximize their exposure.

Notice how they are leaning towards the right? They were reaching toward the sunlight in the window. I just checked on them, and after only an hour they are starting to stand tall and straight.

According to the little class I attended at the USU extension spring fair, seedlings need 12 to 14 hours of light. A timer is useful, but I don’t have a reliable one (our good Christmas tree timer burned out this year, the bad one doesn’t always work). So I’m putting a reminder on my phone until I do get one. Besides, checking on them is a good idea and I want to take daily pictures of them from the same place to document their growth, plus it’s part of establishing a daily habit to attend to the garden.

Early hindsight: I was told on friday (at that class) that I did need a warming mat to germinate the seeds. However, I noticed my first basil seedlings Saturday morning, and my tomatoes in the evening and Sunday morning. The greenhouse cover did a good job of keeping them warm. So I’m not convinced. I did, however, noticed that the seedlings farther away from the window were the ones that popped up first. I suspect the ones right next to the window had the heat leeched out.

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My seedlings are up!

Posted on March 25, 2012 by Ami Chopine

I saw my first basil seedlings yesterday morning and this morning, I’ve seen my tomatoes! The next step is to put them under some grow lights. I was looking around for a shop light for this purpose, but then Vladimir reminded me that he already had some for our garage studio (yes, we’ve made movies in our garage, with a green screen).

The new seedlings. I think the ones that have been mostly closest to the windows have been colder. They're barely peeking out. Those first leaves aren't true leaves, but the embryo leaves from the seed. Pretty cool!

Tomorrow I’ll hang up a light over them. I understand that the lights should be about 2 inches above the leaves. So I should have the light hung on a chain which I can gradually raise as the plants grow.

In other news, I now have a homemade compost bin. I used hardware cloth (wire fence, about 1/2 inch grid), 3′ x 10′. A good compost pile/bin needs to be 3′ x 3′ x 3′ (a bit more than a meter squared) in to decompose properly. You’ll want to bend the poking wires back, for safety. It comes in a roll, kept that wire by some wire wrapped around it. Very convenient because then you can use that wire for ties to connect the edges. At first, I put the ends together with the curve going with the roll. I ended up with a heart shape without the pointy end. So I undid it, and put it together going against the natural curve created by the roll. It’s not a beautiful, perfect circle but it does the job. It’s cheap, light, keeps the pile together neatly, and has good aeration.

My newest garden tool, already working on some leaves and rotten apples.

The leaves are pretty dry, so I also added a bit of water between layers. It’s surprising how many leaves it took just to fill it up that much. There is a lot more where that came from though. A good thing leaves are very light. I am so happy that even the the stuff my yard produces will no longer simply leave in the garbage bin, but will be recycled into the land and go to sustaining the garden and us.

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I ate dirt

Posted on March 23, 2012 by Ami Chopine

Well, actually, tasted it. I read that it was what farmers used to do to test pH. It was just a bit sweet, which means my soil is the pH I thought it was: fairly neutral but slightly alkaline.

My basil seedlings just germinated! I went to a class today on starting seedlings, and I guess a grow light will be needed. And a warming pad? But it’s late. No gardening outside today because I visited the new City Creek Center here in Salt Lake.

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Starting a garden, and a garden journal

Posted on March 22, 2012 by Ami Chopine

March 16, 2012

I’m starting a garden. It’s been a few years since I grew one, not counting the container tomatoes last year. All of my efforts have met with limited success. Lack of experience, lack of keeping up with daily tasks, and a lack of long term commitment.

A few years ago I just decided to give it up to concentrate on other things. But I’ve learned a lot that has now gained critical mass. First, I’m not happy with needing to acquire my food from places which are more concerned about profit than my nutrition or safety. I want to control my food better. I want to have less which needs to be shipped to me – more local food. I’ve come to feel that it’s a spiritual thing too. First, having joy in self sufficiency and hard work. God didn’t put us here in cities. He grew us from nature. We’re part of it, it’s part of us. The human condition thrives more when we are personally responsible for our survival and living among the living things.

I was going to just do tomatoes again this year. But I started an online class, and my project has grown.

March 17, 2012

So, I started a free online class with BYU Independent Study. It’s a personal enrichment class, so it isn’t graded. But it has structure and information. Both of these are very helpful. I have notes I’m doing on my computer, but I’ve been instructed to answer some questions in my journal. A gardening journal is also a requirement of the class. As I learned about journaling my garden, it made a great deal of sense. What did I plant, where, when, when did it sprout, flower, etc. What problems, pests did I encounter and how to solve? Of course! How helpful and inspiring.

Here are the questions from the first lesson.

1. What kind of soil do I have to use? Will it be necessary to add some amendments? (manure, compost, etc.)

A: I have slightly alkaline, clayish soil. I’ll need to add things to make it more fertile and “fluffy”.

2. Is water a problem, and if so, what ideas have I got to solve the problem?

A: Yes. Utah, hot and dry, no access to secondary water. My ideas are soaker hoses, either on sprinkler system, from the house, if possible with a timer.

3. Where can I put my garden? How much space do I have to use?

A. In the garden area, raised, left by the previous owners 17’ X 12.5 = 212 Sq Ft. She recommends 32 Sq ft per person for a good start. This gives me 192sq ft that I need. So there is enough. But I will probably also plant herbs in the front flower bed.

4. With the space chosed, how much sunlight will I get in the growing season in that designated area? Ill it be enough for vegetables?

A. The space is on the south side of the brick wall, but there is a large evergreen tree to the south of it, blocking sun some of the time. I am right now documenting it, to see how much. The house is also to the south – west of the garden. If necessary, the tree will go.

5. How much time can I devote to my new garden and am I willing to check on it each day for five to ten minutes?

A. This has been my sticking point before. Thinking of it as a daily task will help a lot. I think scheduling what needs to happen ahead of time – giving myself tasks and deadlines will also help.

6. Have I completed Chart A with the help from my family and determined what and how much I will plant this season?

A. Yes. I’ll put the chart in a pocket in this journal (I’ll post something here.) But things may change.

7. Have I contacted my local county extension service for gardening information?

A. If by contacting it means, have I visited their website, then yes. But I may drop by the office. I printed out a pdf on what veggies grow well here and their days to maturity here in Utah.

————–

Of course, I’ve jumped the gun. I’ve already purchased seeds: the cold season ones like lettuce, and ones for starting such as tomatoes and onion starts.

I will work my soil and plant lettuces, onions and seedlines today.(I wrote this in my journal. Of course, it got too windy, so I never did get to all of that. Just weeded a little bit) Over the next week I’ll figure out and plant the carrots, radishes, and peas.

Scary, isn't it? You can't tell from the picture, but the soil is nice and dark. Years of dumping yard waste on it have been pretty good, I suppose.

———-

I have planted some lettuce in last year’s tomato planters. I have also worked the garden area, removing some of the grass and dandelion weeds. We have some rotton apples from our tree. Will they be good for compost? I’ve repurposed Chris’s old sand box, the plastic one, for composting. Will it work? Too shallow, or does it let too much light in? Is it big enough four our random yard and kitchen debris?

March 18

Called my mom yesterday. She thought the plastic sand box might not be a good idea. Too shallow. I’ve done a bit of research, and read in the lesson online from part 2. A compost pile should be 3’ by 3’ in order to decompose properly and have a good heat.

Mom also said that she thought the idea of it being on the ground was good. I know I need proper areration. I’m thinking a wooden sloat bin on the ground.

Also read that letting unfinished compost on the ground where you grow will leech nitrogen out. So, the plan I talked about with my mom – to layer leaves and rotten apples directly onto the soil, probably won’t work.

So, where to put the compost bin and what to use for it?

I’ve learned about what kind of gardens there are. I’ll be having a raised bed garden, and some containers. May also grow greens in the front flower beds. Also, broccoli.

March 19

It snowed about two inches in the evening.

Had to displace my daughter and her computer about a foot so it could be in a south facing window.

March 20

Yesterday, I started those seeds I have that need to be started indoors. After some research, I realized they needed a special soiless seed starting mix. There are recipes to make my own, but I don’t have compost yet, nor any other ingredients (do gardeners just keep them around?) So I bought some: Jiffy organic. I will be avoiding pesticides, etc but I may have to use commercial fertilizer. As I read about plant nutrition, I realized I have a lot to learn there. Kind of wish I had a mentor close about.

Anyway, seeds started include: Early Girl Hybrid, Celebrity Hubrid, red Cherry Heirloom, Basil. There are in plastic cells, in a greenhouse kit, on the windowsill of the only south facing window I have.

Plans for this week: keep watch on seedlines, water when “soil” slightly dry. Work on garden area, plant onion starts, radishes, carrots, dill. A bit worried about lettuce mix which has now been snowed on, twice. May rent tiller to get garden soil ready. Plan water supply – soaker hoses, fork valve, with a timer.

I have read that tree roots can take up nutrients. That, plus the shadow, plus the difficulty in getting into our back hard are too many points against it. The tree, alaso, is coming down.

It snowed about 3 inches overnight. Didn’t stay.

March 21

Checked seedlings. A couple of cells may not have gotten enough water and were dry. I added a bit to those. Otherwise, no water needed.

March 22, 2012

Checked seedlines. The moister almost seems self sustaining. Lots of condensation on the lid. It gets quite warm in the day and fairly cool at night. Kirsten*can said her husband uses grow lights for his. My son’s 1st grade teacher said they have some of their science plants just in sunlight and some under grow lights. The ones under lights are much, much bigger and have flowered (they’re quick growing ones). Should I get some? Will hot shop lights work? Or maybe I should just be patient?

Have chosen to do a chicken wire compost bin.

Worked about half an hour yesterday in the garden, another hour today. The wood of the retaining walls is rotting. Hmmm.

The bigger weeds are out, but they were weed grass. I hate the roots from that. It's immortal.

Went to the extension service today, to ask about compost. Master gardener wasn’t there but I picked up a booklet on weeds and their control, since I obviously need it. Also one about homemade quick mix.

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The Wizard of Real Life

Posted on March 14, 2012 by Ami Chopine

I was talking to some friends today while doing my weekly school volunteer stint, about what it is like to be an adult. We weren’t being particularly serious or philosophical. Mostly joking about how we used to yearn to be an adult, and how the things we saw adults do seem magic. We used to want to drive the car. Now its a chore. And we didn’t realize what it meant to pay the bills.

With all of this responsibility, you’d think we felt like adults. But the thing is, we’re the same kids we used to be, we just have to do all this stuff! There was no line that said: now I am grown up. And it’s hard.

I moved out of the house. Nope, not grown up yet because I’m just taking care of myself, barely. Going to school, don’t have a house, still get care boxes that have food and money and my easter present tucked into them.

I got married. Not grown up yet, because I’m still in school and we’re just renting, and I still like ketchup on my eggs.

I got pregnant and had a kid. You’d think this should make me grown up, because now my husband and I are entirely responsible for a child. But we don’t know what the heck we’re doing and we’re scared. Excited and happy, but really feeling our ignorance and lack of experience right now.

More children, now they’re going to school, we bought a house… And somewhere in there, I became an adult. Maybe it was when I realized I disagreed with how the local school system thought I should educate my child. And when I did find a good school system, and realized I was older than some of my kids’ teachers. A lot of me identifying as an adult was when I had to interact with other adults on behalf of my child.

More recently, the last person in my grandparents’ generation died. I have an aunt who has passed away as well, from complications of a stroke. My parents are grandparents of a college aged child. I’m the parent of that child.

But still, sometimes, we joke that we’re just pretending to be adults so that our children, and maybe other adults, will respect us. We’re competent, we can do the things expected of us and that we need to do. But the child we were never left. It just learned how to do all the grown up things. We looked behind the curtain and found the wizard, who was really an eccentric with a lot of machines. And now we’re the ones behind the curtain, pushing the buttons and pulling on the levers.

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Molecular Me

Posted on February 25, 2012 by Ami Chopine

In honor of the new book I’m writing, I’ve started a new blog! It’s about molecular biology, which I love. But I will keep it pretty narrow to that topic and probably not start musing about writing or mothering, or knitting (have I mused about that yet? Don’t think so). You can find it here:

http://moleculesofourlives.blogspot.com/

Also, I’m on pinterest now.

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Information Pollution

Posted on February 16, 2012 by Ami Chopine

Driving down the road one day, I was thinking of things to use in a story when a billboard caught my attention. It had nothing of real use to me, but now my thoughts were on what kind of events radio stations put on and who goes there and why. My mind had gone completely off track from what I’d been thinking about.

Make no mistake. Thinking is work. We input information, we process is, and we output it. It burns up calories and it can make us tired. When we must take information we’ve received and decide what to do with it, we’ve used up a little brain power. Too much of this, and we’ll get tired doing it.
And that’s what advertisers are counting on. After a certain number of viewings, we may choose not to reject it. But no matter what, we are having a choice put upon us that we don’t necessarily want. We never wanted those chicken nuggets, but we’re seeing it every day on a billboard. And every day our brain is trying to prioritize the info: is it trash, or something of use? If something of use, then what do we do with it? Click click, whir whir. You can think of every bit of information we take in as a load that our brain must bear.

But that’s not the worst. Advertisers are using other methods to gain our attention. They use social convention, which is even harder work to overcome. It stresses us out, or gets us excited – when there is no real social gain to be had except a business transaction.
Unfettered advertising is information pollution. While we may need some, I don’t think this widespread distribution is very healthy for us. With the increase in stress and mental exhaustion, we’re less likely to retain information we want, less likely to make rational decisions about things not even being advertised for, and our self control goes down.

We are what we eat, goes the saying. But it’s bigger than that. We are what we input. We seek out much of the input, but much of it is put upon us.

Advertising, the output of information in order to gain a profit, tries to change us. It uses sense of wonder, story, questionable statistics, social pressure, manufactured scarcity or difficulty, and sex to sell things to us – and to our government.

It is true we are responsible for the decisions we make. But in many cases, individuals aren’t even taught the critical thinking skills and the awareness of manipulation that we need to decide against information which is trying to get us to make a choice which will harm us while giving a profit to some company. Then this adds up into many individuals making poor choices, which in turn becomes peer pressure, which in turn influences an entire culture. Once corporations get the government on their side, this effect is greatly increased – even if we see no direct advertising. How many of us are taking in food, supplements, or medicine that we trust because the government has labelled it as okay? We are counting on them to make certain decisions as a single entity, so that millions of us don’t have to do the work over and over again. It’s efficient, but dangerous when hijacked by profiteering or power hungry organizations.

Do we need to know information about things we may want to purchase? Yes. And there may be some things very useful to use which we don’t know about. Advertising is necessary not only for sellers, but for buyers. But I question the methods and ask, do we really need to buy the fatty hamburger being held by the supermodel?

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Opening up Science

Posted on February 9, 2012 by Ami Chopine

I love science.

I don’t have time to do it, really. But I do like to write about it. As I’m getting back into blogging, (realizing that for me it’s work rather than play so I shouldn’t feel guilty about it), I’ve been looking at science blogs. And the first things that have gotten my attention are about how to break open the floodgates.

First off, I read about the journal system from Travis Sanders at The Science of Blogging. Peer review is important for getting quality studies published, but since more and more journals are being published, we can be assured that even poor quality studies get published. What’s wrong with that? Well, no longer can simply being published prove that something someone claims is true. And of those that get published in the prestigious journals where one can probably trust the findings, we still learn little about their quality and why the peer review accepted the study.

Further, readers no longer read entire journals. Since they’ve gone electronic, it’s now possible to pick by subject and read only the studies – across many journals – that touch on subjects you’re researching on, or are interested in.*

Travis suggests a new system, where we have one huge journal where every study can be published with a ‘peer review pending’ status. Then these studies get peer reviewed based on some quality assessment such as a checklist and comments, which are included with the study. I love that last bit. I think it’s an important bit. I’ll tell you why in a bit.

The second interesting thing I read was a post about opening up the journals to us regular folk. And by regular, I mean people with a typical income. Publishers of journals charge so much that we can’t afford to access them. Only large institutions can, effectively closing off high quality studies to the typical person. As a writer, I’ve often found this frustrating. Yes, I can go to my university and access their library, but as a non-student I have to pay 100 bucks plus it’s a decent drive. And that might not even cover everything I might want to research. In this age of information, that’s a little ridiculous. I pay less a year to get free shipping and streaming video from a certain large bookstore corporation.

Some scientists feel the same way, and are starting to boycott the large publishers responsible for such publishing. Thank you!

I imagine a day when things work as Travis says, and such a portal is free or nearly so. Not only that, I think it would be good to have a lay person’s portal attached, with several articles on what makes good science and high quality studies. And if I really could have some wishes, I would want good papers to also include an everyday vocabulary abstract. Something lay people could understand. Lots of science is hard to understand not because of difficult math or concepts, but because of esoteric vocabulary (important in the field, but difficult for the non-initiated to understand.) We just need a simple translation, by people who value science rather than sensationalism.

Add this to the citizen science projects going on – regular people either donate CPU power to cracking large amounts of data, or play games which solve scientific puzzles.

If our goal is really to push the boundaries of knowledge, it’s time we break that knowledge free – free input and output. It’s time we make science a part of the everyday life of normal people, rather than keeping sacred cloisters of elite tinkerers. Yes, I love what scientists do and it’s important to have specialist researchers. But one of the reasons people distrust science is because it is so closed to them.

A large, searchable open publishing paradigm with peer review. These kinds of things are steps in the right direction.

*While I think that it’s fantastic to be able to read only the articles that apply to a subject you’re searching for, I worry that as scientists do this they become even more segregated from each other. There is a lot of knowledge out there, and its inevitable that people become highly specialized just to attack the questions of one small area of science. But sometimes a wider perspective is exactly what one needs to solve a problem. Without the relatively rounded out reading, someone could be in danger of having very deep but very narrow understanding.