Experiments in Life

Okay….I’m gonna get nerdy on you guys….again. I have a blog from a deep sea biology website. And well, since my master’s thesis was on organisms from the deep sea, I thought the blog was appropriate. Anyway, this link will take you to some really cool pictures of some very interesting looking deep sea critters. Just go to the photo gallery and look around. There is even a little blurb telling you more about the thing in the picture. Enjoy.

The Bioluminescence Web Page

Also, another tidbit I found interesting was this:

hydrothermal vents were not discovered until 1976 or so….as one biologist like myself might ask, exactly how much of the deep sea has been explored or sampled since then? Well, someone nerdier than me has figured out an estimate of that. It goes something like this:

ROVS and Submersibles
Total Number of ROVS and Submersibles 20
Total Number of Operational Years 30
Total Number of Dives Per Day 1
Total Number of Lifetime Dives 153600
Total Distance Covered in Each Dive (km) 1
Effective Viewing Distance (m) 10
Area Covered Per Dive (km2) 0.01
Total Area Covered by ROV and Submersibles (km2) 1536

Trawls and Sledges
Average Trawl Distance (km) 1
Average Trawl Opening (m) 5
Total Area Sampled Per Trawl (km2) 0.005
Number of Total Trawls 20000
Total Area Covered by Trawls and Sledges 100

Cores
Core Size (m2) 1
Total Number of Cores 20000
Total Area Covered by Cores (km2) 0.02

Benthic Landers
Total Number of Benthic Landers 20
Total Visual Field (km2) 1
Total Area Covered by Landers (km2) 20

Total Area of Deep Sea Sampled (km2) 1656.02
Earths Surface Area (km2) 150000000
Percentage of Surface Covered by Deep Sea 70.8%
Area of Deep Sea (km2) 106200000
Percentage of Deep Sea Area Covered 0.0016%

Now, isn’t that something !

Note: This information was taken directly from Deep-Sea News. For more information about the above topic, please follow the link.

Here is a somewhat interesting article I found in my blogs. Thought it might invoke an interesting response. Here is a little snippet from the article itself:

The panel concluded that implanting human stem cells into monkey brains “could unintentionally shift the moral ground between humans and other primates.”

Anyway, here is the link to the rest of the article. It merits more research than I have time to do at the moment.

Stem-cell research with monkeys sparks debate: Grafting human cells into animals’ brains seen having ethical ramifications

Well, we have been having technical difficulties here lately….thus the lack of posting. But, things seem to be up and running, for the moment at least, so some updates are in order.

This week started out pretty crappy with a pulled neck. Since then, I have been high on drugs and practically bathing in icy hot in order to get some relief. The end result has been a cranky old woman who smells like a medicine cabinet. I thought I had been doing well with the icy hot smell until I went to a friend’s house on Tues. When the conversation turned to “Oh, I wondered what that smell was when you came in…”, I made a mental note to myself to maybe not use so much next time. Oh well, I got to stay and hang out so the smell must not have been too bad. And I didn’t receive any funny looks at work, except when I was putting more on. I made sure to use up my 4 times a day of icy hot. Aaahhh, Icy Hot! What a wonderful invention. And you know, the smell could be worse. At least it has a minty smell to it.

So, I have been battling a stiff neck all week. Each day it has gotten progressively better. I am no longer doing the full body turn in order to see someone standing next to me….and I can now look at the ceiling without feeling intense pain. As a result, I can now look up at Jonathan with few problems, (you never realize how much you look up until you can’t )

Anyway, Jon has been having a rough time of it too. He hasn’t been sleeping well since last Fri. night. He managed to sleep better last night….meaning he didn’t get out of bed and go play on the computer or read, as far as I know anyway. Hopefully he is coming out of his insomniac cycle for the time being and I certainly hope my neck no longer hurts by the end of weekend. I am unaccustomed to sleeping on my back all night long. I really want to sleep on my side again…but it hurts enough to keep me awake.

Man, what a pair we are. I’m not sure what is going to become of us. I guess we’ll just have to wait and see.

As a software developer, working with abstractions is a part of my daily life. When I am reading a section of code and I see that a particular class exposes the interface for a Factory, I know what that class is supposed to be used for, because I know what a Factory is used for (namely, making things). Likewise, when I am designing a section of code, if I know that the purpose of the code is to make something, I will expose the interface for a Factory because that allows other developers to read my code and know what the code is supposed to do. Making software more readable and easier to reason about is one of the purposes of software abstractions.

In general, when designing a software subsystem, one should choose the simplest possible abstraction that will get across the point. Obviously, the abstraction cannot be any simpler than that or it will not communicate the intent of the subsystem. However, making the abstraction as simple as necessary can be difficult. Is the abstraction simple enough or does it contain unneeded complexity?

What is the point of all of this? While working on the design of a new subsystem, I encountered a place where a particular abstraction would be perfect. The interface for the abstraction was already designed and it was in use in several parts of the system, so it should be readily apparent to others reading my code what it is my subsystem does. Imagine my dismay when the nice, simple, clean abstraction that I remembered no longer bore any resemblance to the nice, simple, ideal. Over the years, more and more cruft had been added into the simple interface that is unnecessary for the problem at hand. Instead of having an interface Foo, I now have an interface FooWithWidgetAndFactory. So, I am torn between two alternatives:

1. Split apart the existing interface into the original, simple abstraction and a new abstraction that extends the simple one (and contains all of the cruft that has been added
2. Implement the existing interface as is and deal with the fact that I will have to implement several methods that will not do anything except confuse the poor user of my subsystem in the future.

Unfortunately, while alternative #1 is the best approach, it is also the most time-consuming and unrealistic of the two (probably several man-weeks). Ironically, if that approach had been taken the very first time this problem cropped up, I probably would not be in the situation of having to choose between the two (since everyone after the first person would have mimicked the first person). So, I suppose I will have to get over trying to do the right thing and choose #2, even though I do not like it.

Still wondering what the point is? I did not sleep last night and am cranky and this just irked me enough into posting about it.

Who would have thought that upgrading to a new DVD player would have been so difficult? For those of you playing the home game, here is what happened. Sunday afternoon, the driver motor on my Panasonic 5-disc HTS died. After doing some research, it turns out that this is a relatively common occurrence with Panasonic DVD players of any kind, not just the particular model that I have. Now, this is not a complete loss. I can still use the HTS as a rather fancy radio and a sound system for the GameCube — it just cannot play DVDs, nor will it ever provide 5.1 surround sound again (since there are neither digital nor analog 5.1 inputs to the system, only stereo inputs). I have come to realize that while the Panasonic was a good starter system — it lasted me for three years — I really do not want to get burned by another all-in-one unit. So, Sunday afternoon I set out on a quest to find a replacement DVD player with the intent of just getting a the player itself and upgrading the surround system with a receiver and speakers at some point in the future.

Now don’t get me wrong — I do my research. I searched many different sites, from electronics stores to review sites, looking for a DVD player that would fit my needs; that is, another multi-disc player that would have a variety of video outputs and at least analog stereo and digital optical audio outputs (I am thinking ahead to a receiver that will handle the Dolby 5.1 that the optical output will provide). Finally, I settled on one that I liked, a Sony 5-disc player whose biggest problem according to reviewers was that it could not shuffle among all five discs, but only in one disc at a time. It was reasonably priced, all I had to do was find it in town, which became the problem. No store had it. Let me correct that. Several stores had the unit as a display: Best Buy, Circuit City, Sears, etc. But not a one of them had it in the store, nor were they planning on getting any more in. My hopes dashed, I turned online. There, I could find it available through Amazon and other retailers, but with a several week lead time. It appears that I had to find another DVD player to fill the void left in my HTS.

After some more research, I found a replacement system. It is an Onkyo 6-disc changer. Now, the difference between the Onkyo and the Sony, beside holding an extra disc, is that the Sony appears to have a better video processing unit, while the Onkyo can perform the mystical multi-disc shuffle that Sony cannot. Also, the Sony supports SACD, while the Onkyo does not. Finally, the Onkyo is approximately $80 more. However, the price difference comes in from the quality of the player — Sony is on the high end of the low-end consumer electronics market while Onkyo is on the low end of the high-end consumer electronics market. However, I was foiled yet again in my attempts to find the unit in town. The only store that carries the unit is Circuit City and they will not have any in for a few more days. Further more, Circuit City (and Best Buy) are extremely misleading in their sales information. From the research that I have done, I have a pretty good idea of the feature sets and specs of every DVD changer that I have looked at in the stores. However, both stores have blatantly mislabeled their products, both online and inside the stores as to what the specs of their changers are. Either that or the manufacturer is wrong. However, given the two alternatives, I would lay the blame on the electronics retailers. I will not go into the kind of service I received, let us just say that I was more an expert on the system than the sales reps.

So, frustrated once again, I returned to Sony’s website where I found a new model of 5-disc changer that looks to be replacing the one that I found originally. Doing a side by side comparison of the manufacturer’s website, along with at Crutchfield, it appears to have a superior featureset to the Onkyo in every respect, except for the shuffle and the lack of support for one disc. But I think I can live without those two features since the price appears just right for me. Now, I just have to find one somewhere. I think that if I cannot find it in town this weekend, I will give up and order it off of the Internet, since it only has a one or two day lead time.

As a side note, I have to admit that I was tempted by the Sony 400-disc changer that was had a similar feature set to the one that I think I will ultimately get. However, even if I put all of my DVDs and CDs in the changer, I do not think I could fill it and I am pretty sure that I would never be able to find what I wanted to watch/listen to in it.

Well, I haven’t had much to write about lately…with the holiday weekend and all, I figured everyone would be taking some time off, so I figured I should too. Anyway, I have been struggling to find something to write about…but, as luck should have it….I recently found some inspiration….meaning I did something goofy

Here goes, I was innocently standing at the water cooler filling up my cup with the sparkling, cool refreshment when all of a sudden, my cup launched itself out of my hand. It hurled itself to the floor and landed before I could catch it. Then, a huge spout of water exploded from the cup. It was….well….it was raining upwards!!! Of course, water went everywhere….and as my luck would have it, I happened to be standing and looking down at the exact spot where the cup landed. What does this mean for the innocent victim you ask…well, it means that I got really wet!! My liquid, cool refreshment splashed all over my jeans, shirt, and one of my shoes. (I’m not sure how I managed to miss the foot nearest the incident…but I’ve learned not to ask questions…just to accept my clumsiness ) Anyway, during the water explosion, the water went so high that the top of my head got wet! When I’m clumsy…I’m really clumsy I looked around to see if anyone saw what I had done, and in doing so, noticed that I was now standing in a puddle. I hurridly cleaned it up and thought I was home free until a coworker rounded the corner. She looked at me and commented me on my jeans. She thought they were the distressed ones because of all the water spots all over my pants. I just said thanks and practically ran back to my cube.

I am happy to say that I no longer have any water spots and I am definitely squeaky clean for the day. However, I do not recommend taking a shower at the office water cooler on a daily basis. People might start to talk

Oh, and I was successful in finally filling up my cup with water and getting it back to my cube without spilling a drop….the sencond time around!!

Hang on tight, you’re in for a wild ride on the biology rollercoaster

Okay. Here’s the deal with the whole I am my own twin thing.

Basically, what happened was the pregnancy started out as a pair of fraternal twins. About 4 days into the pregnancy, the two eggs fused, making one embryo with two different sets of DNA. This results in a condition known as chimerism. (Yes, there was an episode of CSI in which this condition came up and threw everyone for a loop or two!) This condition is pretty easy to spot when the two eggs are a different sex. Usually, the resulting child is a hermaphrodite. There can also be some patterns of different skin pigmentations that can be characteristic of chimerism. However, in the cases we saw referenced, the chimeric individuals were both women, meaning that both the eggs were female. They did not display some of the usual characteristics of chimerism so the condition was not considered until much later.

In one instance, the woman needed a kidney transplant and they were testing her children for matches. They found that two out of her three sons did not match her genetically. In fact, once they started running DNA tests on the extended family, they found that the woman’s husband and brother (genetically speaking) were a perfect match for her two sons. Isn’t that bizarro!!

Sadly, the other case did not go so well. In this poor woman’s case, she was applying for welfare and they needed to do a paternity tests on the children. Well, they tested her DNA against the children and they found that her DNA was different than her children’s. Well, her children were very young and everyone jumped to conclusions. They figured she had kidnapped the children and was trying to commit welfare fraud as well. They took her kids away and she was stuck trying to explain to the DA that she was their biological mother. No one believed her. Luckily, she was pregnant with her 3rd child at the time. And luckily, this child did not match her genetically either. She got her kids back and she was diagnosed (not that it’s a disease mind you) with chimerism.

In the case of both women, the two sets of DNA were dominant in different tissues. By blood tests alone, it was not obvious that two sets of DNA were present. Only by taking other samples, such as hair, saliva, and organ samples, were doctors able to discover the second set of DNA.

It was a pretty interesting show to watch. I suggest watching the actual show if you get a chance. It would probably do better explaining it in laymen’s terms than I can. I think Jon still has questions as to why they didn’t figure it out sooner. I am having to brush the dust off my books in order to answer those questions….if there is an anwer.

This condition is quite rare. There are only about 40 cases known worldwide if I am remembering the show correctly. Of course, documented cases more than likely consist of the pregnancies which produce a hermaphroditic child. Who knows how many of us out there could be considered our own twin And what does this do to the reliability of DNA testing, especially when used to solve crimes? Who knows…..only the future will tell

Hope you found that as interesting as we did. Tune in next week, same time, same channel, for another lesson in the wonderful world of biology

By the way, did anyone watch the twin thing I posted about earlier? Or is the suspense still driving everyone crazy?

Is anyone still curious enough to want to know the answer?