Exploring “Crazy” Watermelon Genetics

The other day there was an interesting discussion about watermelon genetics that started on the Alan Bishop Homegrown Goodness plant breeding forum from a fellow who lives in Australia. Turns out Watermelon genetics are sort-of complicated, but interesting.

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Approx. Watermelon Flesh Color Spectrum, from most dominant to most recessive.

The discussion started by asking about which traits in watermelon were dominant, mostly referring to flesh color but also open to other traits as well. The original poster mentioned that he started his own mass cross of over 30 watermelon varieties together (a grex) in preparation to developing his own landrace adapted watermelon to his Australian climate. He said this past season he planted only the seed for any F1 hybrids from any yellow fleshed watermelons he had but got about 90% red fleshed watermelons and concluded that obviously red-fleshed watermelons were dominant. The interesting thing is they are BOTH dominant AND recessive at the same time! Yes, watermelon genetics is a little complicated to say the least, lol.

Wait… what??!… haha yes, you did read that last sentence correctly. Red-fleshed watermelons are both dominant to yellow-fleshed watermelons AND recessive to yellow-fleshed watermelons. Turns out there are actually TWO different kinds of yellow-fleshed watermelons.

Watermelon Flesh colors range from various forms of red, pink, yellow, orange, and white. So how does one figure out what is recessive and/or dominant over what? Turns out most of these have already been studied and we can interpret that data. I’ve recently resurrected my old website domain and turned it into a plant breeding wiki of sorts. Feel free to check it out @ www.biolumo.com. The main resource i am using is the wonderful watermelon genetics info posted online by the Cucurbit Genetics Cooperative hosted by North Carolina State University and in particular Todd C. Wehner part of the Department of Horticultural Science at North Carolina State University. http://cuke.hort.ncsu.edu/cgc/cgcgenes/wmgenes/gene12wmelon.html

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From the data available we can come up with a rough basic pictorial based diagram. I like pictures; they help me understand things better. Basically there are at least two types of red-fleshed known as “Scarlet Red” and “Coral Red” in addition to two forms of yellow-fleshed known as “Canary Yellow” and “Salmon Yellow”. Turns out Canary Yellow is dominant to all other forms of color. Scarlet Red is dominant to Coral Red, Orange, and Salmon yellow. Coral Red is dominant to Orange and Salmon Yellow. Orange is dominant to Salmon Yellow. You get the point. And basically seems to work in a cascading effect of “more color” to “less color”.

I personally prefer the taste of the Canary Yellows over most red/pink, though there are still some good red ones out there! What i don’t like are the Salmon Yellows (and maybe orange). To me and in my climate the Salmon-Yellow watermelons have a weird mealy and/or mushy texture and have a muted / poor flavor. By contrast the Canary Yellows seem to be really sweet and might even get sweeter more easily / earlier in a northern and colder climate like mine. That is just my personal preference, your taste buds and soil conditions may differ.

Now this is a general simplified version. There are a few caveats however. Such as the fact that there is a Canary Yellow inhibitor gene that when present will turn a Canary Yellow back into a red that is hiding underneath. Also the fact that there may be a few other minor colors that have not been studied yet such as “dark red“, “rose” , and “pink“. It is possible that these colors are just minor variations of the former reds and function the same way from “more color” to “less color” in terms of dominance. It is also possible that if these are indeed separate shades of color that they may buck this trend and function in completely different ways from different biochemical pathways. Hard to say at this point. But i will leave the possibility open either way in case new studies in the future address these watermelon flesh colors.

Oh, and what about white-flesh?! Yes that’s right, we have completely forgotten to talk about white fleshed watermelons. Oh, you didn’t know there were white-fleshed watermelons? Yeah there are. They are not generally as common but there are white fleshed watermelons out there. Turns out white-fleshed is a little more weird. Let me explain.

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F2 Generation of White-Fleshed Watermelon Genetics

 

White-fleshed watermelons are currently being studied more in depth in China and a new paper is due any time in the near future. But until then all we have is the data gathered already from a past study on it. According to that study: white-flesh were found to be dominant over all color. In an F2 (Second Filial) Generation the ratio is: (12 white : 3 canary-yellow : 1 red).

Pretty interesting huh? Yeah, basically if i interpret this information correctly is that for whatever reason white flesh overrides color. In the wild, watermelons were originally thought to be white fleshed and low in sweetness. This is certainly the case in the wild citron melon (Citrullus lanatus var. citroides) which has hard white flesh and bland flavor. The bitter apple melon too (Citrullus colocynthis) but it obviously is very bitter.

The genetics for watermelon at this point captured my interest so i decided to find out what i could about seed coat colors. If you thought watermelon flesh genetics was complicated, you’ll find the genetics for watermelon seeds is a nightmare. Nevertheless i waded knee deep into the confusing data and came up with some generic info that i think can give us a basic trend that we can use.

WatermelonSeedGenetics
Approx. Watermelon Seed Coat Color Genetics

The genetics for watermelon seed colors and patterns is a nightmare. Truly it is. Partly because the studies we have don’t all agree and we don’t have examples of what these old researchers were really studying. One person’s “tan” might be another persons “light brown”, etc. You get the point. Very subjective. But based on the studies we have it basically looks like in general there are three genes working together and we can come up with a basic trend that we can follow.

Basically black seeds are dominant to other colors. Brownish or greyish seeds with a particular black mottling striping with black dots is next in line. Tan or brown seeds are probably next in line. Green seeds (not pictured here and rare) are dominant over red. Red seeds are the most recessive except for white. White seeds are the most recessive and recessive for all three gene combinations. This is a very simplified interpretation and there are probably actually more than three genes. In my population i have grey seeds which is not a color that has been studied. Also i have no idea what “tan” actually is so i lumped it in with brown. Brown too has not been studied, nor has “reddish-brown” among others.

Watermelon_fruit
Watermelon Fruit Shape is Co-dominant. Elongate (OO), Oval (Oo), and Spherical (oo).

Watermelon Fruit shape is relatively simple however. Yay! Simple co-dominance at work. Two long genes (OO) give you long fruit. One long gene and one round gene (Oo) or heterozygous gene pairs give you medium oval shaped fruit. And two copies of the other round gene (oo) gives you round spherical fruit. Easy peasy!

Golden-rind fruit are easy genetics too. Simple recessive (go). This is a trait more common now as it helps people identify when a watermelon is ripe. They turn bright yellow when ripe.

Watermelon_yellow_rind
Yellow-rind fruit are recessive (go). Fruit become golden yellow as they mature.

And the last trait i will mention is the “explosive rind” trait.

Haha, it’s not as scary as it sounds, but it’s not particularly a trait you want in your watermelons. Fortunately it is recessive and hopefully you wont encounter it in many varieties. I’ve seen it in the unusual striped variety but fantastic tasting ‘Osh Kirgizia’ watermelon, but otherwise not that much. Officially explosive rind (e) causes the fruit rind to burst or split when cut. This is true, but i also find that often when this trait is present the fruits themselves have a higher rate of splitting open while ripening on the ground and even when you lightly grab one to harvest. Not a trait that a market grower would want. For a small backyard gardener it’s not a huge deal as you can eat them right away, but still a slight inconvenience, especially if they split in the field and ants get to them. Black ants really do love sweet watermelon flesh.

Watermelon split
The recessive explosive rind trait (e) causes watermelon fruit rind to burst or split

 

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Preview: Upgraded Bread Machine Incubator TR444 [in progress…]

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Ok. So! Back to hardware / electronics projects!! Yay!

This is a preview for an upcoming post. I am currently working on upgrading my Hacked Breadman Breadmachine TR444 Incubator from a previous project. I’m adding some RGBW neopixel LEDS from Adafruit for light. It will have a button to change lighting sequences from White to red/blue to purple, to blue, to black. All the colors one would need to 1. see into the machine. 2. Color LEDs to grow seedlings for gardening. 3. blue which may come in handy for bacteria cultures? IDK. maybe not. But whatever. I currently have the arduino code for the light sequence working.

I will also be adding a fan for circulation. I 3D printed the fan holder. I may or may not have a button to control the fan. I will have a big red button to start the incubator cycle (37 Degrees C for bacteria / fungal petri dishes). And i am considering another button for a programmed Dry Heat Sterilization routine. As mentioned before, according to Wikipedia:

The proper time and temperature for dry heat sterilization is 160 °C (320 °F) for 2 hours or 170 °C (340 °F) for 1 hour.

I also think i will be integrating my Chronodot real-time clock for use with this dry heat sterilization routine and possibly some other incubating cycle as well. Cool! Fun stuff! Lets get working!!

p.s. post in the comments if these are the kind of projects you’d like to see more of of! 🙂

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Gardening with Conductive Helical Coils 2016

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So despite the blog and my internet presence being quite mute as of late i actually have been up to quite a lot. My homemade Lulzbot Mini 3d Printer this summer was a success, amd i have constantly been improving it. At some point i will take some photos of it’s final progress. A few of my pea breeding crosses from last year were successful, including one i’m excited to grow again which is a cross of the Purple Passion dark purple seeded pea (which is a small genetically weak pea variety) with another stronger pea variety. That should produce something really cool in the coming years. And this fall and next spring i’m experimenting with school by going through a Precision Machinist course and am learning how to use milling machines, lathes, and CNC equipment to produce Aerospace quality components. Not sure if that’s something i want to do long term, but they are skills i’m interested in and can use throughout my life. So that’s new.

Anyway though, as a throwback or a revisit to my post in 2010 titled “Do Plants Really Need Sunlight?“, which has actually been one of the most visited posts on my blog over the years, i finally got around to building a few of those coils that sounded so interesting.

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Conductive Helical Coil around the stem of a plant

So the basic premise or idea behind using a coil of wire with electricity is that it produces a small amount of electricity or a magnetic current through the air. This is the same idea Nicola Tesla was after all those years ago when his imagination was captured with the idea that everything could have wireless electricity. And in many cases his dream has come true with an ever increasing amount of technology these days using induction to wirelessly power or heat things. The basic premise of applying this technology to plants comes from an article i read once that talked about how researchers were able to measure a small direct current from trees in a forest by placing nails in them. They then had ideas about placing nails in many trees and hooking them up together to power small electronics like a battery or cell phone charger, or a smoke alarm. Basically all plants (and maybe all living things) produce a bioelectric field of energy. If one can tap this field to harvest electricity, then why cant we tap into it and feed these plants with extra electricity to help them grow.

One question i asked in my old blog post was if plants even need sunlight at all as long as they are getting some form of energy to grow. I still haven’t done an experiment to test that idea, but it’s still an interesting question. Because it makes me wonder if there are ways plants could be grown in complete darkness.

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Regardless, this summer i finally built a prototype plant coil. I built it rather late in the season, so i really wasn’t able to give it a good test. My original plan was to plant 3 or 4 genetically identical tomato plants near each other in the relatively same soil with at least one plant being the control. I was then going to observe over the course of the summer f the tomato plants within the coils had larger and better growth than the control. That was plan anyway, i just didn’t quite get to it.

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You can see here we were trying to use a volt meter and another coil to see if we could detect that our coils were working. We weren’t having much success with the meter in the beginning and i don’t remember if we did later after increasing the power supply a bit. But in theory you should be able to measure with a second coil.

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I placed it on three smallest tomato plant clusters in the very late planted tomato patch. Interestingly enough, the three plants it happens to be on might be the only three blue tomato genetic varieties that survived my haphazard tomato disasters this year. Since placing the coils on these plants i have noticed an improvement in them and they have since catched up to the growth of the other tomato plants in that spot. Although at the same time i did also make a furrow and started watering them more. But even so i’d be willing to go out on a limb and say that the coils did help them go from “runt” status to catching up to the others. I may yet get a few tomatoes from the larger two before winter hits. Thanks to Gilbert for providing the motivation to actually build this project. And a thanks to the Homegrown Goodness plant breeding forum where i get so many of my adventurous gardening and plant breeding ideas. You guy’s are the best and a continual inspiration to me. Read more: http://alanbishop.proboards.com/thread/8623/breeding-tower-potato-ideas-wanted?page=13#ixzz4LoiDtFZE

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So, while my experimentation was a bit haphazard this year i think i still did ok. It was a fun project that went from an interesting patent to a cool project idea in my head and at the back of my mind, to a fully functional project / prototype. Plus i think these coils look cool. haha.

But it makes me wonder what other cool patents are out there that i can exploit, reverse engineer and build to experiment with. One of my next projects i think will go the opposite route and will be heavily steeped in Open Source as i think i will try and build a “Food Computer“. Basically it’s a small climate controlled aeroponic grow box. It should allow me to continue my plant breeding efforts even in the winter which is really what i want. Plus it will allow me to learn more about this “urban gardeng”, “vertical gardening”, and “aeroponic” stuff. I can’t wait to get back to pea, bean, and tomato breeding even though the summer and fall are waning fast. I think i’m going to repurpose my 2ft x 2ft t-slot frame that i was intending to turn into a large 3D printer and/or CNC mill. But it’s still going to be a long time before i finish that project, so i figured hey why not actually use it for something useful in the meantime! So.. that’t the plan.. 😀

 

 

Project Updates November 2015

80/20 1020 Extruded aluminum t-slot y-axis 3d printer bracket
80/20 1020 Extruded aluminum t-slot y-axis 3d printer bracket

The first update is that i’m still steadily designing new parts in solidworks for my custom 3D printer. This photo is one of two y-brackets that will hold the 1020 size t-slot extruded aluminum (from 80/20) y-axis beam. It looked good in Solidworks, now it just needs to be fabricated (3d printed) into a real-world working part (as with many other parts).

Y-bracket for custom 3D printer
Y-axis bracket for custom 3D printer

It’s really fun designing parts and then seeing them become real functional parts. Recently I’ve even been looking into a local program for CNC machinist training as a job. Apparently there is a large shortage of qualified CNC machinists in my area along with a booming and returning engineering and manufacturing hub here in the area.

While i was designing new parts and fitting them together i found a few minor problems with a few of my old designs being off and not lining up properly with the 1020 extruded aluminum. So i spent some time fixing that and cleaning them up a bit. Good to find those errors on the computer first than after i make the parts.

I received the prototype PCB’s for the XYZZY Motor Controller 1.0, The downside is I’ve found numerous errors that i missed, so I’ve been trying to fix those. But then to compound those problems the main circuit itself has a problem where the HIP4081A h-bridge chip circuit is only driving a motor (in this case a test load LED) in one direction. At first it was shorting out the other direction, but now i think it just loads the current down and does not activate one side of the hbridge. It’s actually driving me crazy trying to fix it and find the cause of the problem, but it’s still quite a mystery. Perhaps electronics is just not my thing. Perhaps i really should give up on that project after never being able to have good success. But i don’t know.

In plant breeding news: i was able to harvest three corn cobs this year. Two were decent sized purple husked corn cobs, the other was a good multi-colored flint. The third one had lots of kernel color diversity, it even had several speckled kernels, and chin-marked ones, and even some that had both speckles and stripes! I recently found purple sweet potatoes at Whole Foods and i will be trying to sprout one and grow my own slips for next year.

I was also able to grow a few good squash this year, some good progress on the pea breeding, and an excellent year with Joseph’s Watermelon Landrace. Sorry, i didn’t get good photo’s of the watermelons, but i had some excellent red sweet watermelons and some good yellows as well. Especially for Northern Colorado, the watermelons are the plant breeding project i’m most excited about and ironically having the best success. Can’t wait for next year! And all this despite it being an incredible difficult and strange gardening year!

Rediscovering 3d CAD because of 3D Printers

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This past week (maybe 2) I’ve been utterly obsessed with 3D printer stuff. It has gotten me excited about 3D drafting and CAD all over again. Simply because you can create a 3 dimensional object on a computer in a matter of minutes or hours and render it to look completely realistic, but now because of 3d printers you can actually make those objects (if you so wished)! Awesome!

Yesterday and Today I’ve been playing around with Solidworks again. My ancient 2007 version of solidworks. lol. But it works non-the-less. Although i’d love to try out Autodesk 123d Design (which is free). But, why oh why are there still no good CAD programs that run nativity on Linux. Especially if you have a Mac version. If it runs on Mac it can easily be ported to Linux. Why do you think the Arduinos and the rep-raps, and open-source, and so many other great things have taken over the world by storm? Yes it’s because they are great products, but also because they are cross-platform! Okay, End-Of-Rant.

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But Seriously, i actually really like designing something in CAD if it’s something i’m excited about. Today i ventured into the realm of something relatively simple, test tube racks. But sadly there are not currently very good designs for test tube racks available. Which actually surprised me. The three best places I look for pre-made CAD files are at 3dContentCentral, which is the oldest site of this kind that i ever encountered. It is mostly for people who use solidworks, but the great thing about the site is that it has a tool that can convert to and from many different CAD formats, including solidworks formats, IGES, STEP, STL, etc. The second is GrabCad. GrabCad is a new community also aimed at engineers sharing CAD models freely. It dosen’t have the nice file converter that 3dContentCentral has, but it has a vibrant community that provides feedback, help, and will check out your designs. Someone on GrabCad actually helped render the nice  looking wood rendering of my 1950s style test tube rack. How nice! Thank You! And the third is the famous MakerBot Thingiverse. Thingiverse is less focused on CAD formats and instead is focused on creative designs optimized for 3D printing. At minimum an STL file will be available for anyone to download and print on any 3d printer they have access to. I currently dont own my own 3d printer, but am currently using the Lulzbot mini that currently resides at my local library. How’s that for public access?!!

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So these are the three test tube racks i modeled today in Solidworks. Not super amazing i suppose, but i’m proud of them. My favorite is the nice wooden 1950s style test tube rack. I partly chose to start with that one because i have one that looks just like that looks like it was made by a monkey in china. It seriously is not as nice as my virtual one and not anywhere near as fancy looking either. But also because it is the standard test tube rack featured in the banned 1960s DIY chemistry book: The Golden Book of Chemistry Experiments. It was just begging to be brought into the modern world.

I then ventured into modeling a simple test tube rack because there were none available that i liked. I may make a smaller version of this one for 3d printers that have small print beds. Perhaps one with only 4 test tubes.

The last one i modeled after a nice round plastic test tube rack I’ve seen on the internet. I don’t have one, but I’ve been meaning to buy one. But i wanted to model one in Solidworks and create one that fit on a Lulzbot mini 6″ X 6″ print area that other people could print out too. So i made one of appropriate size and then made it able to split in two to be printed easily. I really like how the design came out. I hope to be able to test it out by printing my own sometime.

1950s Style Test Tube Rack:

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Economy Style Test Tube Rack:

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Round Mini Test Tube Rack:

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Interfacing Vernier Sensors and Arduino (and vice-versa!)

So, recently I’ve been bored. That’s nothing new really. The up side to the times when i get really bored is that i usually end up starting some sort of electronics project. Since i have an interest in the DIYBIO movement and an interest in DIY chemistry i have realized that it’s really cool (and helpful) when you can use sensors to collect your data. But up until now i haven’t had the motivation (or the money) to really dive into it. But today’s post may be the beginning to turning that tide.

Awhile back i stumbled across this post by David Hay, after noticing this question on adafruit. In it he tinkers a bit with interfacing an older vernier (light?) sensor with an arduino clone.  Since i use vernier sensors in my chemistry classes at school i have come to love them. I wondered if i could do something similar, but what i really wondered was whether i could do the opposite as well. Could i interface other non-vernier sensors (like sparkfun sensors) using an arduino to the fancy LoggerPro software or my TI84+ calculator? It turns i can!

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The LoggerPro software is really good stuff, but i’m cheap whenever i can be. That’s one reason i thought of my TI84+ calculator. I already have one of those, and vernier has released free software for it that can graph data from vernier sensors in real time. The program is called EasyData and can be downloaded here. The second option is to use LoggerPro on Linux. And since i’m already a full time Ubuntu user i get to use the newly updated free LoggerPro beta for Linux! Sweet Beans!

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I’ve already tested both. They both work great. The cool thing is that i was able to hook an arduino to my calculator EasyData program and also LoggerPro on the computer by using a Vernier EasyLink (with an adapter to convert it into a GoLink). I had to get a Vernier Analog Breadboard Cable for it to work, but it was well worth it. I sent some test pwm values using the Arduino example code for the fading led on arduino digital port 9. I used the example pdf from the DIY Light Intensity Sensor example project on the Vernier website to help me out a bit.

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I was also able to do the opposite like what David Hay did with his sensor. I was able to successfully interface a stainless steel temperature probe from Vernier (which is basically just a thermister in a nice case) to my Arduino. I used the example pdf from the DIY Build a Temperature Sensor example project to help me out, along with the values in an equation provided in the manual that came with my stainless steel temp sensor. I also bought this nice Analog Proto Board Connector from vernier which allowed me to do this so quickly. Here is the code i used on my Arduino to calculate the temperature from this thermister.

*/
int led = 13;

#include <math.h>

#define ThermistorPIN 0 // Analog Pin 0

float vcc = 4.91; // only used for display purposes, if used
// set to the measured Vcc.
float pad = 15000; // balance/pad resistor value, set this to
// the measured resistance of your pad resistor
float thermr = 20000; // thermistor nominal resistance

float Thermistor(int RawADC) {
long Resistance;
float Temp; // Dual-Purpose variable to save space.

Resistance=((1000 * pad / RawADC) – pad);
Temp = log(Resistance); // Saving the Log(resistance) so not to calculate it 4 times later
Temp = 1 / (0.001129148 + (0.000234125 * Temp) + (0.0000000876741 * Temp * Temp * Temp));
Temp = Temp – 273.15; // Convert Kelvin to Celsius
Temp = Temp / 2;

// BEGIN- Remove these lines for the function not to display anything
//Serial.print(“ADC: “);
//Serial.print(RawADC);
//Serial.print(“/1024”); // Print out RAW ADC Number
//Serial.print(“, vcc: “);
//Serial.print(vcc,2);
//Serial.print(“, pad: “);
//Serial.print(pad/1000,3);
//Serial.print(” Kohms, Volts: “);
//Serial.print(((RawADC*vcc)/1024.0),3);
//Serial.print(“, Resistance: “);
//Serial.print(Resistance);
//Serial.print(” ohms, “);
// END- Remove these lines for the function not to display anything

// Uncomment this line for the function to return Fahrenheit instead.
//temp = (Temp * 9.0)/ 5.0 + 32.0; // Convert to Fahrenheit
return Temp; // Return the Temperature
}

void setup() {
Serial.begin(9600);
pinMode(led, OUTPUT);
}

void loop() {
float temp;
temp=Thermistor(analogRead(ThermistorPIN)); // read ADC and convert it to Celsius
Serial.print(“Celsius: “);
Serial.print(temp,1); // display Celsius
//temp = (temp * 9.0)/ 5.0 + 32.0; // converts to Fahrenheit
//Serial.print(“, Fahrenheit: “);
//Serial.print(temp,1); // display Fahrenheit
Serial.println(“”);
digitalWrite(led, LOW);
delay(1000); // Delay a bit…
digitalWrite(led, HIGH);
}

So what does this mean? I think this opens up a whole new world of possibilities. On the one hand i believe i can now use the nice Vernier LoggerPro or EasyData real-time graphing software to interface non-vernier sensors like Arduino boards directly and perhaps others like a Sparkfun Alcohol sensor? (which i have one i would like to try) This should make it easy to interface cheap sensors in chemistry and biology labs that already have vernier equipment. I think it also means that we can now easily use Vernier sensors on non-proprietary devices such as cheap Arduino micro-controllers.

I also look forward to soon tinkering with using an Arduino webserver as a different real-time sensor graphing and data logging device. I hope in the future i can help to create other tools which might be useful for DIYBIO and other DIY science.