Week 14 The Bone eaters

I am being a little too literal in interpreting the assignment, but I figured if I need to pick an animal that I know NOTHING about, I should pick one I never heard of before. How should I look for such a mysterious animal?

I started with remembering our whale skeleton. Shawna was telling us how lucky we are to have such a specimen. Lucky indeed! I had heard rumors that it is much more difficult to acquire a dead whale today. Thank goodness we recovered it when we did. The reason is that now we know that there are whole whale decomposition communities with species that are only found on dead whale carcasses in very deep water. Today a dead whale is more likely to be towed out to sea to feed the critters at the bottom of the ocean. We have only become aware of the complexity of whale-fall communities in the last 10 years. It is likely that many species from that community have gone exinct in the last 200 years due to whaling (http://books.google.com/books?id=hKoUnp_YaPAC&pg=PA345&lpg=PA345&dq=whale+carcass+decomposers&source=bl&ots=UEDfein0BD&sig=w0hLeWP9fDVoGMB6vY74ZOOY_wA&hl=en&ei=Kz_VS9OlOcH6lwfXhK3MCA&sa=X&oi=book_result&ct=result&resnum=7&ved=0CBcQ6AEwBg#v=onepage&q=whale%20carcass%20decomposers&f=false )

In 2004, one genus was discovered that decomposes whale bones, Osedax . http://www.mbari.org/news/news_releases/2004/whalefall.html

I choose one of those-- Osedax frankpressi
Phylum Annelida , Class Polychaeta, Order Canalipalpata, Family Siboglinidae .

The family includes the giant tube worms that are found near deep sea vents. http://en.wikipedia.org/wiki/Siboglinidae

The Osedax species' nearest relatives are those deep sea vent tube worms. This makes sense. None of the adults of this family eat. All of them are dependent on symbiotic bacteria for their energy needs. DNA studies have shown that the whale bone decomposers diverged from the sea vent tube worms 30 to 45 million years ago, just as whale-like creatures started inhabiting the oceans. http://www.biomedcentral.com/1741-7007/7/74  .  Evidence of Osedax "feeding" activity has been found on whale bone fossils that are 30 million years old. http://www.sciencecodex.com/boneeating_worms_30_million_years_old

Here are some pictures and a video of present day Osedax:  http://www.hartnell.cc.ca.us/faculty/jhughey/Files/osedax.jpg,

http://www.mbari.org/news/news_releases/2009/osedax-spp/osedax-spp-images.html

Here is a diagram of Osedax:   http://spineless.ucsd.edu/NewFiles/Osedax.gif

These "worms" consist of a tube with feathery tops. The bottom of the animal consists of roots that burrow into the bones of whales. The roots contain Oceanospirillales bacteria. These bacteria produce enzymes to hydrolyze collagen. http://rspb.royalsocietypublishing.org/content/275/1633/387.full
Cholesterol, fats, and collegen in the bone are thought to be food sources for the bacteria housed in the roots of Osedax.

All of the visible adults of this genus are females. This was a mystery for a while until it was found that males were tiny, almost larval, forms that attach to the inside of the female's tube. The live off the energy provided by their yolk sac.    It has been postulated but not yet proven that larva that land on bones become female and larva that land on females become males. http://www.biolbull.org/cgi/content/full/214/1/67  . The females produce copious amounts of eggs http://www.springerlink.com/content/k5053278k5m86733/ . This also makes sense, because once the bone pile has disappeared finding the next dead whale on the vast sea floor must be a daunting task.  The larvae are microscopic trochophore that can swim 9 to 16 days. That hardly seem long enough to find a new carcass.

week 12 - factory farms and other version of CAFO's

Fourth week in a row for blogging. Thank goodness I can finally get a rest next week.

Every doctor I have ever had, has always given me the lecture that I shouldn't take antibiotics for colds because they are viruses. Many years ago I had a doctor explain the evolution of bacteria to me, telling me that antibiotics will become useless if we use them when we don't need them. Thus we will create resistant bacteria.  I believe it, but what is the use when we are having wide-spread, uncontrolled daily use of antibiotics on our food animals. What is the point of humans being judicious in our antibiotic use. (Well, yes, there are lots of disease in the human population that are not in the food population. Still...)

It is not like they are making disease-free food-animals. the antibotics are often given because the animals grow faster with them than without them. They are also given because our food animals are grown in un-natural concentrations and are being fed food that is unnatural for them. This makes the animals more vulnerable to disease.Our butchering/processing of animals exposes a lot of bacteria and spreads it from one carcass to another, so we are not talking about creating a product with less transmissible disease.

mutation or acquisition

Here is a great twist. Instead of mutating genes to produce the enzymes you need, just aquire some novel gut flora.

http://www.sciencedaily.com/releases/2010/04/100413072046.htm

Evolution

Blogging AGAIN. This is messed up but since I missed class last week, I missed any discussion that would have clarified the problem.  Week 8 was for blog group 1. Week 9 both groups blogged Genetics problems. Since Blog group 1 did week 8, it should have been group 2 week 10, but group 1 went again and a few of us group 2's also went. I don't want to miss points so guess I better blog this week TOO.

There is a vast amount  of evidence from all realms of science (chemistry, genetics, geology, etc) that support evolution. There is more evidence than any one person could ever study in one lifetime. I have heard one student tell Shawna that scientists that believe in evolution  just started with the wrong set of assumptions. Unfortunately, that is the kind of sound bite that evolution denyers can easily spout. The body of evidence on the evolution side could take years to absorb and is not so easily distilled into compelling sound bites.

We seem to be stuck in a period much like that of the time of Galileo. Galileo was kept in house arrest for supporting the Copernican  idea that the earth went around the sun. This idea was against the thoughts of the church at the time and he was tried by the inquisition. And yet religion continues today even though almost everyone agrees that the earth moves around the sun. We know the laws of gravity that create the orbits of the earth, the moon, and our satellites, space shuttles and space stations. Though the "church" felt threatened by these ideas in the 1600's, the church is still here and it no longer denies modern astronomy.

Week 10 - Bring in the clones

Is cloning pets a good idea?

Well, if people have more money than they know what to do with, I suppose it is better than them going out an buying hummers or adding more square footage to their house.  I guess if the owners realize they are not getting the same pet, it might be an option for a family that has neutered a pet but now want offspring.

How does cloning effect our ideas of death?

This is really a fool's game. The clone is just a copy of the genetic material that created the pet. It is not the pet itself. Until we can clone all of the memories, history and thought processes of the cloned individual we still do not have Fluffy. Fluffy is still dead. On the other hand we do need to start thinking about what is life and what is an individual. I have read about the possibility of duplicating or downloading every thought and thought process of a human into a computer. we can't do it now. Our computers are still quite primitive. But what if it were possible 500 to 1000  years in the future? If my "mind" were downloaded into a computer, would that be me. Do I need my body to be me? Some of these futurist ideas are explored by Ray Kurzweil in a book called "The Singularity is near" http://www.singularity.com/ .

Would you clone your pet?

No. It is hard. I miss Fiji terribly. she slept in our bed every night for 16 years. We had a relationship with her, but a clone of her would not be her. First she would not look the same. Yes, the clone would probably still be a 9-pound, polydactyle calico, but she wouldn't look like Fiji. Being calico, different patches of black and orange would occur during her fetal development.

The clone wouldn't remember the games we played or special memories we shared. ah,,, you say I could teach the clone all the same things, but is that really the same thing. I could probably teach a cat from the pound some of the same things. you might say that i attribute too many memories to a cat. I remember things we shared.... like the time in her youth when, dog-like, she would jump in the car for a ride to the post office with me. Her adult self had already forgotten these tricks... so the memory is just in me, not in the cat. How do we know what their memory capacity is? Their minds are different than ours, but we often anthropomorphize their motives, feelings, thoughts and memories.

Maybe it is the mystery of what our companion animals think, that causes us to consider cloning. I could hope I could get Fiji back, just younger. It is somewhat less of a mystery what our human companions think. At least sometimes the human companions tell us their thoughts. No one thinks they can replace a child, a brother, a parent, a lover, a mate with a cloned human. Unless or until we can clone the mind, we cannot ever approach replacing a lost companion, human or animal. When we can clone the mind as well as the body then we will be in a scary realm of playing god. HMMM.... Ah.. the mind is the thing. If you could clone my mind and put it in a different body, I bet my mind clone would think it is me, even if the shell of the body  looked different.

On the other hand, in the future, ( for the super-rich) maybe we do not have to clone the whole pet. Maybe we just clone new kidneys, heart, and liver for our pet ; find cures for pet cancers and other aging processes and just keep the original Fluffy alive indefinately.

Other thoughts:

For more information on why cloning will not bring back the pet, see this Nova special on epigenetics. It talks about natural clones of human twins and how their gene expression changes over time, making the twins different. In other words, even clones are not identical. http://www.pbs.org/wgbh/nova/sciencenow/3411/02.html  there is also a picture of a cloned cat that looks nothing like its mother/sister.

Food cloning
OK Cloning a pet is one thing, cloning our food animals is quite another. The biodiversity of our food is becoming more and more narrow. This is a very, very bad trend. At least there are some seed banks trying to preserve some diversity, but that is really not the same as biodiversity on the ground. Our apples are already clones. The fact that our turkeys can no longer reproduce in the natural way is disturbing. Most of our pork comes from artificial insemination as well. [I am not saying that artificial insemination is cloning, just that cloning would give the ag-industrial complex greater control over the "product"]. The multitude of pig and turkey varieties that went to market a hundred or less years ago have been reduced to 1 or 2 marketable varieties, made for mechanized production, processing and marketing. They are no longer animals but instead are manufactured, fairly-uniform products for the supply chain. (well, the animals still think they are animals and probably still don't liken living on CAFOs. Oh here is an evil thought: Taking a page from the book  "Restaurant at the End of the Universe", we can program or breed animals not to care about living on a factory farms.)  For a cheesy television version of the "dish of the day" check out this You-tube: "Restaurant at the End of the Universe" .

Week 9 Genetics

OH.... I guess I was supposed to post something myself instead of just commenting on everyone else's post.

so maybe I am cheating since I have had elementary statistic which includes probability theory. This genetics problem set is not too dissimilar to probablity theory ( tossing coins and dice and stuff.)  

On the other hand, there are a lot more difficult problems to solve in this arena that are not in the problem set --- like traits that are on the same chromosome near each other and therefore are not completely independently selected.

---

DOMINANCE OF GENES ON the X chromosone ???!!!

I do have a question on sex-linked attributes on the X chromosome. Take an individual who is heterozygous for a trait that is on a autosomal chromosome. If the phenotype of that individual is an expression of one gene on one of the chromosomes, we say that gene is dominate. In this case every cell in the body has two chromosome Dd, the chromosome D is expressed.   This is our definiton of dominance.

OK. But take a sex linked trait like orange vs. black cat. Our problem set says that yellow is dominate over black. I do NOT think it is technically correct to say one color is dominant over the other when the color is on the X chromosome. A male cat only has 1 X. Therefore there is no question of which trait (which chromosome ) will be expressed in the phenotype.  If the X has the yellow (orange) gene, the male will be orange. It it has the black gene, it will be black.  There is no dominance in this relationship. Whatever gene is on that X is going to be expressed.

So what of the female of the species. She has two X's. This is similar to the autosomal complement. If she is heterozygous for orange/black and if you say that orange is dominant, then you would expect an orange cat. This is not the case. In order for females to not have more active genetic material than males of the species, one of the X's is permanently inactivated in a Barr body sometime in the developmental stage of the organism. Thus for every cell in the female cat one of the X's is permanently disabled. Therefore, there is still only 1 functional X chromosome per cell just like male cat cells. That is where you get the calico coloring in cats. Some patches of cells on the cat have an active orange gene X and some have an active black gene X.   Therefore there is really no chance for dominance to occur because there is only 1 active orange/black gene per cell.

The red/green color-blind X-based seems like the same problem. some of the cones in a heterozygous woman would be color-blind and some of the cones would not be color-blind, depending on which X is disabled.  On the other-hand, it may be ok in this instance to say that non-color blind attribute is dominate over color blind. It is not true at the celluar level, because one X is still permanently disabled. However, according to this research, some of the heterozygous women with a mixture of color-blind vs non-color blind cones actually have better color recognition than other people. (http://aris.ss.uci.edu/cogsci/personnel/kjameson/assess.pdf ). This one surprised me, because I thought I had heard that women that were heterozygous for red/green color blindness had less color sensitive due to the mixture of color-blind and non-color blind cones.

Week 7 - Energy of organisms

Can humans function using anaerobic respiration? No

Are there any times when humans do rely on anerobic cellular respiration? Yes, muscle cells can use anaerobic respirations when they run out of oxygen. (that is, when they are using energy faster than oxygen can be provided.) However, don't try this with other cells in the body. The energy requirements of central nervous system neurons are so high that even a brief period of hypoxia (from stroke, stangulation, etc) and the subsequent lack of ATP will cause rapid cell death.(http://www.neuropathologyweb.org/chapter2/chapter2aHIE.html)

ATP's of fermentation is a net of 2 per glucose vs. 36 per glucose molecules for aerobic respiration. So aerobic respiration is 18 times more efficient. So yes eukaryotes have more energy available to them.

reptiles, fish, birds, and mammals all use the same aerobic respiration. They are all running on that 18 times more efficient system than yeast in a anerobic environment. So why are cold-blooded less active.  Well it is said that fish are cold-blooded. Who is surprised, since it must be hard to maintain temperature in a media with the heat capacity of water.   BUT the fastest fish, the tunas,  are somewhat "warm-blooded"(esp, their swimming muscles). So warm-bloods move faster????  You witnessed the effect in the yeast lab ( yes, even those prokaryotic, cold-non-blooded yeasts.)  In biological systems, for every 10 degrees in temperature, the rate of chemical reaction is doubled. That is, until you raise the temperature far enough that you denature the enzymes. As long as you do not denature the enzymes, you can get energy twice as fast by raising the temperature 10 degrees.(of course, this is dependent on being able to supply substrate and in this case oxygen fast enough to keep up with the reactions.)

 A small fraction of this speed is due to the kinetic energy of the molecules involved. A greater amount of the speed is that the "heat" overcomes some of the activation energy. So it is not surprising to see lizards out basking in the sunlight.

Don't try to raise your body temperature 10 degrees to get energy twice as fast however. Our enzymes are tuned to work at the constant temp around 98.5.