I haven’t been giving computers or linux much attention on my blog for awhile. I hope to remedy that situation soon. I am eagerly awaiting the Ubuntu 12.04 LTS release in a few months. It feels like I’ve been waiting forever, but once it is officially released i hope to give it a thorough review.

A few weeks ago i decided i couldn’t wait and i did an early upgrade from Ubuntu 10.04 LTS to the 12.04 alpha release by using the command “update-manager -d”. I’ve been using Ubuntu 10.04 since Canonical replaced gnome with unity (which at the time sucked). Sticking with an LTS release turned out to be an excellent choice and provided a stable production machine. I think it’s something i will do again in the future.

The upgrade appeared to go really smoothly. Actually i think it’s the  smoothest upgrade I’ve ever done. Everything transitioned well into the new environment. A few nice things stuck out when i first started using it. The first was the new and polished unity interface. I must say that this experimental interface has come a very long way since it was first introduced to ubuntu. In fact it has matured so well and works great that i actually now prefer it to the old Gnome desktop. And i was pretty pissed-off when i heard they were ditching trusty ol’ Gnome for a relatively untested and early interface. I actually used the first Unity implementation on Ubuntu Netbook Edition. I thought it was crap, and i haven’t used any form of it until now. I actually think the new and updated Unity interface makes it easier for me to get productivity work done. It just feels right. But I expect to see some changes to it by the time 12.04 is officially released, so we will see.

The second thing i noticed was Firefox. Okay, so Firefox hasn’t changed much, but i finally have an updated version. For some strange reason Firefox in the 10.04 repos hasn’t seen any updates in a while. Although i may start to be liking Google Chrome better. But i still like firefox for some things (like the ability to block flash ads), and the range of add-ons.

The transition from OpenOffice to LibreOffice seems a bit silly, since they are pretty much the same product. I do like the green and white logo though. But, i dont blame the forking of LibreOffice from OpenOffice since there was quite a bit of doubt that Oracle would be playing nice with opensource. I don’t know that much about what eventually happened, but i think Oracle turned OpenOffice over to the Apache foundation, so i would think that the two could merge back together someday. I don’t really care what anyone calls it though, all i care about is if it works well. And it does work fantastically well.

UbuntuOne has also matured, and I’m finally getting the hang of synchronizing folders between computers, which i like A LOT. I’ve never used DropBox before, but i understand the two services are very similar. I choose to use UbuntuOne because of the integration with ubuntu though. And I’m glad to hear that a new windows client has been released. Synchronizing folders across all kinds of different devices just makes sense, and reminds me that we really are living in the future. Just like that phrase in The Time Machine, “The Future is Now”. I look forward to hearing about other ubuntuone clients for macs and android phones, etc.

The only con i have to report is that my sound was broken upon upgrading. I reported it as a bug, so hopefully they will fix it. Other than that i don’t have anything else to report.

Unfortunately I’m not using my 12.04 alpha system anymore, because shortly after upgrading i accidentally hosed my whole system. I was trying to remove some program in the terminal with asterisks (*) and –purge, and somehow apt started removing EVERY program from my whole system. It must have been some sort of dependency hell thing. I was able to stop it before it finished, and i was also able to use an alternate-install disc to use “fix broken system” to reinstall unity and apt-transport-https (which is a critical file for apt to be able to download packages), and ubuntu-desktop, and some others. But i was not able to restore the system to fully functioning order. The shutdown and restart buttons stopped working correctly, and the login menu didn’t work right either. I was forced to back-up my data and reinstall (i think 11.04) from a cd. I look forward to a fully stable and official 12.04 release soon.

Here’s an excerpt:

Zea mexicana plant grown in N. Colorado (October 2011)

I grew some Teosinte again this year. I was able to plant several different varieties, so i could evaluate them and observe their differences. There seemed to be more differences than similarities, and there were a few traits that were common with some of my Indian Corn that i like to grow. One interesting trait that i occasionally see in my indian corn is where there are some male parts that grow on the very tops of the cobs that in theory could produce pollen to self pollinate. The problem with this trait in corn is that it usually doesn’t seem to function anymore when it does show up, and in most cases never appears at all.

Zea mexicana silking and setting seed in N. Colorado (October 2011)

Here is a “cob” of Zea mexicana teosinte that has made it to the silking stage and is ready to accept pollen. I’m delighted to have found a variety that has the potential of setting mature seeds here in my garden. Teosinte is native to Mexico, so there are quite a few differences in the length of the growing season between Mexico and Colorado. So far only Zea mexicana and a variety of teosinte called “Northern Tepehuan Maizillo” are the only types to reach the pollen stage here in Colorado; and Zea Mexicana is the only one so far to reach the silking/seed stage. I look forward to trying to grow (and maybe cross) both these varieties next year. This Zea mexicana plant is really close to producing mature seeds, but the plant is dying due to a frost the other night. If i can start some Zea mexicana earlier in the season, then i might have a better chance of getting some mature seeds before winter.

I grew a very nice specimen of Zea diploperennis last year, and i hoped it would be able to survive the winter, but it did not reappear this year. I planted some more, but they were in a nutrient deficient spot, and had stunted growth this year.

Distribution map for teosinte growing areas

A theory of mine that I’d like to explore sometime in the future has to do with the origin of Corn (Maize). Teosinte is obviously the origin, but there are significant differences in seed shape and cob formation. My current theory is that cobs are an emergent trait that appeared after two distinct teosinte lines crossed. The most likely cross in my mind is one between Zea mexicana and Zea parviglumis. Their ranges come very close to overlapping in several areas. After growing several varieties in my garden this year, i can tell you that strangely Zea mexicana and Zea parviglumis are eerily similar to corn. Zea parviglumis is a tillered teosinte, but it has only has about 6 tillers, but other varieties like Zea diploperennis or Zea huehuetenangensis have like 10 tillers each. Zea mexicana has no tillers. Zea parviglumis is a little short, and Zea mexicana is fairly tall. Theoretically if they were crossed then the resulting hybrid should be the same height as the corn that grows in my garden, and the intermediate growth pattern should also be closer to corn than either parent.

Teosinte hybrid showing an emergent but primitive 4 rowed cob

Part of my idea of an emergent cob from a teosinte hybridized with another teosinte species is based on the work done by Mary Eubanks. Mary Eubanks has published a few articles about a theory that Gamma Grass (Tripsacum) is one parent of modern corn that hybridized with teosinte a long time ago in Mexico. It’s an interesting theory, but it seems that most geneticists don’t believe Tripsacum is a parent that led to corn. I also have my doubts about it, but the the work done by Mary Eubanks is still important. She has created Tripsacum-Teosinte hybrids at Duke University.  Her work shows that when teosinte is hybridized with a similar grass species (Tripsacum) that in F2 generation a primitive 4 rowed cob starts to form and is an emergent trait.

Diagram showing postulated evolution of modern maize

Surprisingly there don’t seem to be a lot of pictures of teosinte on the internet. If your interested in seeing a few more pictures of the ones i grew this year in 2011, then by all means visit my photobucket page here. The pictures of teosinte are not individually labeled as to which species is which, but i can tell them apart after growing them.

Zea mexicana grown in N. Colorado (2011)

EDIT (October 24, 2011): I was able to hand pollinate BOTH the Zea mexicana plant and the Northern Tepheuan teosinte in my yard today with the pollen from the Zea mexicana. They only have about a day and a half before a big snow storm, so i hope it’s enough time to actually fertilize the seeds. I will try and cut the plants down and bring them inside to dry. Here’s hoping!

Northern Colorado isn’t exactly known for having a climate that is hospitable to growing watermelons. In fact, I’ve tried planting and growing watermelons at least three times before, each time ended in a miserable failure. This year was different though in part by my determination to succeed and the landrace method i recently discovered. A landrace is basically a mix of a bunch of seeds with lots of genetic variability. That variability makes it easier to locate a variety that is already at least partially adapted to my climate. While some (or many) varieties in a landrace die off immediately, some usually survive. And the theory is that by selecting only the best ones year after year, we eventually get something that is really good. Much of my inspiration for this project has come from Joseph Lofthouse who has had success with a cantaloupe landrace in utah, the breeding work being done by Rebsie Fairholm in the U.K., and indirectly Carol Depp who i believe inspired the two people i just mentioned. I keep hearing people mention her breeding books, but i have never read them myself.

This is where my experiment with this idea comes into play. I’ve always liked eating watermelon, but the common belief here in Colorado is that they are hard to grow (if not impossible). There is at least some merit in that belief. I myself have failed previously on three separate occasions to cultivate Mark Twain’s angelic food. The biggest problem was that i never used the right varieties. In a sense i guess you could say that the landrace method is basically a shotgun approach. When in doubt, shoot everything!

And while this is only the first year i have attempted this project, i feel the results so far have been extremely encouraging. This is the first year i have ever gotten any ripe watermelons, which in itself is a milestone. I got dozens of them. Many of them were tiny though, like baseball tiny. Some of those tiny ones actually ripened though, and a few tasted really good. I also got some that were of decent size too. I tried my best to select varieties that were mainly Northern, Native American, and short season varieties. My hope was that some might already be adapted to the temperature requirements, some adapted to the soil, pests, etc, and they would be able to cross pollinate with each other, so i could eventually select for one that has all the best traits.

Even with this criteria probably a third of them did not ripen properly, and went directly into the compost pile. But, i was able to harvest a few really good ones, and few OK ones as well. Something that was interesting though was that many of the early ones to ripen were yellow-fleshed watermelons. I had included some seeds from a few that were supposed to be yellow, and i had heard myths of yellow watermelons, but i didn’t really think i would actually be able to grow my own. The first yellow i ate was probably the best watermelon i’ve ever tasted. I didn’t know the yellow ones tasted better than the red ones! I’ve found out that there might actually be three different shades of yellow watermelons, and i think i saw all three this year. What’s remarkable though is that one of the yellow types is a dominant trait, while one is a recessive trait.  How crazy is that! I suspect that the yellow ones might be able to ripen better here in my climate than many of the red ones, but maybe it was just a coincidence. only time will tell.

Anyway, yeah. This whole landrace breeding is pretty darn awesome! I hope to continue selecting the best of the best, and maybe eventually i will have my own special variety that grows vigorously here in Northern Colorado. If you’d like to see a few more pictures and details about this breeding project, then please visit my website at biolumo.com.

GLIMANTA KIEL ORO

La unue kanto de Katharine Brownshire (MANEKENO) de Pensilvanio, Usono. Ĝi estas pop-muziko kaj elektronika. Kati diris ke ŝi volas “krei bonan muzikon kiu allogos por junuloj, kaj esperantistaj kaj neesperantistaj, tra la tuta mondo.” Kaj ŝi celas emociigi junuloj pri la esperantista kulturo per bonega muziko kiu placxos tiel kaj tiom kiel nacilingva muziko. Sendube gxuste tion sxi faros. http://manekenooficiala.com/

La Bambo

Esperanto versio de la kanto “La Bamba”. La Bambo kantata de JoMo kaj amikojn (en la KD “JoMo friponas”, eldone de Vinilkosmo).

Pli ol Esperanta Muziiko:  http://www.vinilkosmo-mp3.com/

Google's logo showing a dihybrid cross, but failing to follow the law of independent assortment (yellow pods & yellow seeds are not linked), and also failing to show that yellow seeds are dominant. But, it does show the 3:1 ratio of green:yellow pods in the F2 generation.

After noticing that Google’s logo today was in honor of Gregor Mendel’s 189th Birthday, I decided to make a post about pea breeding. On first thought pea breeding doesn’t sound all that interesting. Even to people who are interested in plant breeding in general. I myself thought that Mendel had already worked with all the interesting traits found in peas out there, but i have found that i was wrong. I’m starting to find that the traits Mendel worked with are actually very neat in person, and the ones he didn’t know about are even more interesting.

The Google logo itself is actually a visual representation of Mendel’s experiment of crossing yellow podded peas (recessive) with that of green podded peas (dominant), but it also shows his other experiment of crossing yellow seeds with green seeds. Unfortunately it looks like Google’s logo is not following the law of independent assortment and is showing linkage between yellow pods and yellow seeds, which is incorrect. Yellow seeds are actually dominant, so Google fails in that regard. But, even so it illustrates the ratio of 3:1. In other words, in the F2 generation 3/4 of the offspring will be green-podded and 1/4 yellow podded.

yellow-podded pea also with the constricted pod gene (Golden Sweet)

The picture above shows a variety called “Golden Sweet” which remarkably has both the rare yellow-podded gene, but also the gene for constricted pods. After growing this variety for the first time here in my own garden, i can see why Mendel was so fascinated with pea traits at the time. I personally think his experiments were directly inspired by this unique variety of pea, which is suspected to have become close to extinction in Europe and the rest of the world, until it was accidentally rediscovered recently in a collection of seeds from India. It certainly is a pea with some interesting genetics.

I’ve only just started to experiment with crossing peas this year. While it sounds like it would be hard, it’s actually fairly easy. But, it really does help to have a tiny pair of scissors instead of an exacto knife or scalpel. The only hard part is that pea flowers are self fertile and self pollinating by nature, and you must catch the flowers very early to be able to cut off the immature pollen so you can use pollen from another plant. I really don’t know how Mendel did that in his day in age, but i applaud the man. Here are two links to pea breeding on Rebsie Fairholm’s blog.

How to breed your own garden peas
How to hybridise garden peas 

Mendel worked with several different pea traits, and documented at least seven of those. Yellow-podded vs Green-podded, Yellow-seeded vs Green-seeded, Inflated Pods vs Constricted pods, Round seeds vs Wrinkled seeds, Tall vs Dwarf, flower position, and flower color.

Several Pea Traits I'm Currently Researching (I'm actually researching more than seven)

'Midnight Snow' snow pea (purple-podded mangetout / edible-podded pea)

The Unusual Parsley Pea

Hyper-Tendril peas! (aka. semi-leafless peas)

Alan Kapuler of Oregon discovered a while back that if you outcross a pea called “Parsley Pea” which has an insane amount of leaflets on it’s tendrils, that you can get a pea that has hyper-tendrils and has twice the amount of tendrils and doesn’t require a trellis to support themselves.

Rebsie Fairholm's famous red-podded pea

Rebsie Fairholm from the U.K. discovered just a few years ago (2008) that when you cross a purple-podded pea with a yellow-podded pea you get a red-podded pea! How awesome is that!

Biskopens (rare red-seeded pea)

I’m currently trying collect lots of pea varieties with rare and interesting traits, but one that is uniquely rare though is one called Biskopens. It is the only pea that i know of that has red seeds! Yeah, it’s a red-seeded pea!

Purple Passion (rare purple-seeded pea)

This is a very rare variety i was lucky (and surprised) to get in a recent trade. I really look forward to growing out this variety next spring. Supposedly it also has purple pods. I have no idea what it’s origin is. I’m curious if it’s the same gene as the red Biskopens pea, but perhaps with a green seed underneath so maybe this one comes out purple? I’m just speculating at this point.

.

If you are still interested in all of this, then please feel free to visit my pea_breeding webpage to find out more detailed information about pea genetics and about Mendel’s work with peas (as well as  and Rebsie’s red-podded pea). Or my recently updated webpage about the seven-ish unusual pea traits that i’m currently studying at http://biolumo.com/peas.html.

Red Corn Pollen / Ruĝa Maizo Poleno

[en]

For those who don’t grow Indian Corn or any unusual plants for that matter, your missing out. Most people don’t even know that corn kernels come in different shades of colors, and probably even less know that you can also get red/purple pollen, red or purple stalks, and even purple leaved corn plants. The genetics are amazing. Peas also come in interesting colors of yellow, purple, and red (seeds and pods).

[eo]

Esperanto Kemia Perioda Tabelo de la Elementojn.

[Eo]

Mi finis tradukanta tio versio de la “Perioda Tabelo de la Elementoj” en Esperanto hieraux. Mi decidis uzi la vorto “Kaliforniumo” kaj ne “Kalifornio”, sed “Kalifornio” estas tre mallonge. Mia esperanto ne bonega, do bonvolu diri al mi, ĉu se mi tradukis vortojn malĝuste.

[En]

I finished translating this version of the Periodic Table of Elements into Esperanto yesterday. I decided to use the word “Californium” instead of “Californio” even though the second one is much shorter. My Esperanto isn’t that good, so please tell me if i translated anything wrong.

.

[English]

I finally leaned how to buy a domain name, and figured out how to use Ubuntu to host a website. It’s really interesting. On the one hand, starting my own website isn’t as hard as i thought it would be and is quite liberating, and on the other there are so many technical things associated with it that it’s actually harder than i thought it would be. So technical in fact that it approaches the very upper limit of my computer skills.

The Domain i bought is BioLumo.com for those who are interested enough to check it out. Be aware that my HTML skills are rather crude, and at the moment i’m hosting it myself, so it could very well go down at any moment. The name was chosen to attempt to be understandable by both English Speakers and Esperanto Speakers. Bio Luminescence in English, and Bio Illumination in Esperanto.

Anyway, so what does it actually take to create a website? Well, first you have to get over the idea that if you think of a website name that nobody else has ever thought of, that in theory it should be free. Strangely enough you MUST purchase a domain name from a Domain name registrar. The one i chose after reading several reviews was name.com. They have decent prices and good reviews. So yeah, you buy a domain name and pay a yearly subscription fee, or you can pay for more years in advance.

2. You need someone to host your website. I eventually don’t want to go to all the hassle of hosting my own website in the future, so i will probably pay someone else to host it. I’m thinking people who are computer geeks and open source fans. Yeah, Laughing Squid looks like a great place to host. They also seem to have awesome price rates on their cloud servers (Amazon EC2?).

This time i set up an old Ubuntu Computer to serve as my webserver. It took a bit of work. Not too much, but a little bit. I had to install Apache and FTP. I had to configure a few other things as well. The hardest part was trying to set up the permissions on the /var/www folder, because otherwise my server locks everyone out from accessing my website files.

Anyway, yeah. This is the first time i have ever had my own website. Hope i can figure out some cool stuff to put on it.

[Esperanto]