Sunday, September 21, 2008

Proteins Are Surprisingly Cool!

When you think of proteins, you may think of things like meat and fish and beans...not little tiny molecules of protein. In biology, we've been learning about the little guys (protein molecules), and man, are they COOL. It's almost like science fiction. I have to marvel that man has been able to figure out and document all this stuff. I have to further marvel that something so interesting can be so well tucked away, hidden and obscured by bad writing and needless complexities. It takes me a good long while to unpack the interesting concepts from my incredibly dense textbook, which is clearly, CLEARLY not written by actual writers, but by scientists.

So, in simple language, what is so cool about proteins? Alot of things. For starters, there are 6 things a protein can do on the surface of a cell. So imagine a cell in you, or in your favorite cat, or whatever. You probably already know that cell has a plasma membrane around it. What you may not know is that proteins can embed themselves in that membrane and then serve some very useful functions. The shape of a protein determines its function. Some of the neat tasks it can perform:

The protein can act like a little tube, or channel, letting stuff in and out of the cell - a little passageway through the membrane. Actually, the protein can also "gate" the channel, only allowing certain things through or out of the cell. Even cooler, the protein can open one end, take something in, close itself, and then let it out the other side, so that the boundary between the inside and outside of the cell is always secure, but selected stuff is being securely transported from one side of the cell to the other.

Proteins can also attach to the cytoskeleton of the cell, sort of the framework of the cell, and provide some structure. They can perform like a little pump, taking in Nacl (3 molecules at a time) and pumping out potassium (2 molecules at a time) in a rotation, moving 5 molecules per transaction, and performing up to 60 transactions per second!

Proteins can also act like sentinels, alerting the cell to the presence of substances or signalling from the cell to other cells. Proteins can attach to other cells as well, in a neat little interlocking way like snapping lego together.

Proteins can also act as catalysts, or enzymes, and speed up some chemical processes. A protein can have a special site on it, called the active site, that something else (called a substrate) fits into. The protein tightens around it, stressed it's composition and changes it into something else. (For example, it might remove an electron, break a bond, or otherwise make an alteration to the substrate). There is a tiny on and off switch too, to let the protein known when to stop working. And, proteins can line up in a little chain called a biochemical pathway where the first guy makes what the second guy needs and the second guy makes what the third guy needs and so on until finally whatever the cell needs is manufactured. It's a tiny assembly line! And what's more, you have to have those to get energy and to use the other stuff in your body that you need to live.

It's truly amazing! They have diagrams of it all - but even cooler, they have actual photos of some proteins. Wow. I mean, WOW! Think about it - 75 years ago no one would have thought we could photograph a protein. Technology is so neat; there are benefits beyond Tivo, as good as Tivo is!

Proteins fold into shapes - the simplest being a helix, like a curly phone cord, or like a folded sheet, sort of like a furnace filter. Scientists are working on figuring out how proteins fold. To see some cool images of folding patterns and read an article on that, click here. They have four levels of complexity in folding, and can get pretty complicated looking.

It doesn't take long to conclude that life is not possible without proteins, and that these super amazing tiny machines are just brilliant little things that have oh so cleverly adapted themselves to do what needs to be done. The only thing more amazing to me is that both my textbook authors and my instructor have managed to take STUNNINGLY COOL STUFF like this and make it completely dull, boring, confusing and even downright inaccessible in some cases. In the end, I think the book authors are smart and were trying - and if I try really hard I can eventually understand what they are saying, but then I find myself wanting to rewrite the whole chapter because it could just be explained so much better!

Anyway, if you get bored, google proteins - look at the pictures, read a little bit, and I bet you too will gain a new respect for these itty bitty workers which reside in all of us.

Saturday, September 20, 2008

Wolf De-Listing on Hold

You probably already heard - but the government has decided to withdraw de-listing plans for now, thanks to the results of a court decision against the federal government. The plan was too extreme, and withdrawl of it will send the government back to the drawing board. The sad thing is, in the short time the wolves were without protection, some were killed. Idaho's population is 350 wolves lower than expected, even without a hunting season taking place. While shootings will likely not account for the total decline, hopefully the reasons can be explored.

I believe that wolves have a valuable role to play in the ecosystem as top predators and they should be left alone. The fact that man wants to live in wolf habitat areas should mean man lives with wolves, not eliminates them. But, even if we accept hunting as a valid means of population control (which I don't, other than for the sake of argument) allowing hunting poses some real problems. It's hard to tell males from females, so it will be hard to contol which sex is killed. Alpha pairs usually do all the mating, and it can be hard to identify the alpha pair. If one or both alphas end up getting killed, the pack will fragment, actually making wolf/human conflicts works as wolves spread out rather than stick to a given and established territory. Breeding will also be massivly impacted, so the choice to kill one wolf may have ramifications far beyond that one wolf.

In addition, wolves are providing a valuable service in keeping chronic wasting disease out of Yellowstone National Park. One pack is primarily responsible for this, taking down weak and sick animals and patrolling an area just outside the park boundry. Wyoming's plan to kill all wolves outside of Yellowstone would be a disaster for this pack and in turn, for the wildlife of Yellowstone.

It is too bad that man has such a huge prejudice remaining against the wolf. It is a beautiful animal and has a valuable role to play - as do bears and other predators. It's offensive to see how rabid people can be in their hatred of another species.

Hopefully this "time out" will allow the government to re-group and be a little more rational, examine the genetic breeding distribution and options between packs, and consider something less than the Wyoming "kill them all" crap ass managment plan. I will be very interested to see how it all goes, and it's nice to have a little good wolf news for a change.

Saturday, September 13, 2008

Dog's Eye View of Agility

A cool video gives you a great view of an agility course from the dog's perspective. Wow!

Leopard Eats CROCODILE?

Check out these amazing photos. Wow!!! A leopard taking down a croc is unbelievable!

Thursday, September 11, 2008

Even Though I Know They Don't All Make It....

While I love Africa more than anyplace else I've been so far, it's always a place of extremes. The highs are so fabulously high they are incredible - and unbelievable. But the lows can be absolutely heartbreaking. I don't forget either extreme, and one tempers the other.

For some reason I have been thinking about this lioness lately. I saw her in a park in northern Botswana in rainy season in February of this year. While everyone was excited to find a lion, it was pretty clear when we got close that this one wasn't going to make it. I have no idea what happened. She appeared to be a young female, alone rather than with a pride. She was very, very thin - emaciated. Whether this was because she could not hunt alone, or had a sickness, I have no idea. It was rainy season so the animals were more spread out, but there were a variety of them, including young baby herbivores, so it doesn't seem like lack of prey would be the issue.

Her skin hung around her in folds, and her bones jutted out. She looked up at me and her eyes were still bright. She had a lot of life left, her eyes hadn't clouded over and she hadn't given up yet. But, it was clear she was in some distress, and she seemed very tired. She did not move or get up other than to turn her head.

It would have been nice to be able to help her. Of course, there was nothing I could do. I didn't think she would last the week, and by now she's probably long since gone. I wonder how she was separated from her family, and how she came to be alone and so darn thin. Even though I know they don't, and can't, all make it, it is so hard to come across an animal that is on the way out, and not be able to do anything about it at all.

It was bittersweet. A few minutes later I saw one of the most fantastic sunsets in my life. As I watched the blazing reds, the flaming orange, and the pinks and purples over the savannah, I thought about her, still lying there, not far away. I wished that I could comfort her, at the very least. I was only with her for a few minutes, but the memory of her is still fresh, and comes back to me at odd times.

Saturday, September 6, 2008

Grizzly Man: A Special Kind of Crazy

If you haven't yet seen the disturbing movie "Grizzly Man" you might want to consider Netflixing it. I've been thinking about it lately because there is a new 8 part series on Animal Planet called "The Grizzly Man Diaries." I've been watching it and I think that it is a good idea to watch the movie first so you have more context. It's been interesting, sick, and sad all at once.

If you aren't familiar with the story, Timothy Treadwell was not a scientist. He was a guy who had a drug problem and then overcame it and found something he loved. That something was bears. He fell madly in love with them and came to see himself as their champion and protector. he spent 13 years in Katmai National Park, Alaska, observing and filming them. He kept a diary, sometimes in video and sometimes written. He took photos. The problem was, he saw himself as some sort of Jeff Corwin, absent the education of course, and also some sort of bear survivor and extra special person. He clearly had a variety of mental problems and these come through much more in the movie than the TV series so far. It can be hard to watch and listen to him as he talks about how great he is and how one with the bears.

Eventually Treadwell acquired a girlfriend and she was camping with him in Katmai in 2003 when tragedy struck and they were killed and consumed, by bears. If you want the details of what happened, they are on this website. There is a "fake" audio of the attack floating around but it is a hoax. The actual audio - and there is one - has not and will not be released and it supposedly pretty darn awful because there is a ton of screaming, as one might imagine. It was not the bear's fault. In fact, the true miracle is just how much Treadwell got away with BEFORE he got killed. Thirteen YEARS of walking up to bears, petting them, etc. and NO PROBLEM. Death was inevitable with the kinds of stupid risks he took - the amazing thing is just how often the bears turned away or tolerated him or expressed kindness and acceptance.

I suppose part of why I find Treadwell hard to watch is that I can so well understand the pull he had towards animals. It's just that he didn't have the inner strength or perspective to step back and see the big picture sometimes. For example, he set his tent next to a fox den and he habituated foxes. He named the first fox Timothy after himself. He loved walking through the park, a fox on his heels. And who wouldn't? I would LOVE to cuddle baby kits as he did, to tame wild foxes and to hang out with them and be their friends. It would be FANTASTIC and I get why he was drawn to do that. The problem is, it's awful for the foxes because not all people can be trusted. To be wild and remain safe, the foxes have to fear people - the reality is that there is a very severe risk that if the foxes were not afraid of people, they could be shot, assumed rabid or otherwise "not acting normal" and the best thing for them is NOT to get socialized. But I do get why he did it.

Another thing I completely understand is his interference. He views the animals as his friends and he cannot stand to see them harmed so he will often interfere. He knows it is wrong. He knows that he is not really studying natural behavior if he interferes and alters that behavior. But he can't help himself - he consistently messes with nature, intervenes, and in the process, takes risks that seem insane - any may well be - but which he sees as necessary. For example, he might charge and try to scare off a bear being aggressive to one of his "friend" bears. Crazy? Yeah, but in a way I have to admit I totally understand.

I would take nearly any risk to help a wild creature in need, and I have come close to doing things just about as dumb. In Africa when I see an animal in a snare or trap or with a thorn or infection, it is usually only the guide that keeps me from trying to help. Once in my own backyard, I was really stupid and never even cared. Callie was at the back yard barking like mad her "ALERT!!! INTRUDER!!!!" bark. Two stray male un-neutered pit bulls were in the back yard. I didn't let Callie and Simon out to chase them off as I would afraid they would get bit. But the cats were out and I had to protect them so I went out back. One of the pits lunged for Lizzie and actually knocked her off a fence. She was literally falling into its jaws and somehow I managed to tackle the pit around the neck and Lizzie managed to vault over the fence again, seeming to defy gravity in the process. I threw myself at the pits until I had them leashed and I took them in to the Humane Society where I was met with sheer shock. "Why didn't you call animal control?" the woman asked. "Why would you ever risk doing this yourself?" Honestly, I never thought one second about it - Lizzie was in trouble and I was not about to let her get hurt. If I myself got horribly harmed in the process I would not have cared. Is it really so different to charge at a grizzly bear to protect one you love? I think not, so I can't really fault Treadwell for this even though I know rationally it makes no sense.

He does develop a complex thinking he is the only one who cares or who can help the bears, and he does get a huge ego and talk on tape about how much BBC or whatever media will pay him. He seems to think he knows what he is talking about even though he has only read things about the animals from books. Not that he didn't learn a lot about them - but not like he was a true authority to anything other than his own observations either. That I can't relate to, but I do understand how he could fall so in love and end up feeling alone, like he was the only one who cared. He was paranoid, and he didn't follow the rules of the park or behave rationally.

Treadwell sees hard things - nature. Animals killing other animals. Natural, but awfully hard when you get attached. He takes sides. Again, he is so NOT a scientist, but a guy who is a bit off his rocker, editorializing and interacting and changing outcomes and not doing what is truly best for the animals sometimes. His heart was in the right place but he failed to think things through.

He saw other people and tourists as intruders and he did not like them. I can relate to that too. I can also see how wildlife tourism promotes wildlife conservation, though, and see that there is still enough space to get away from people if you try, thank goodness. But it's eerie to me that I can understand this aspect of him. Is he just someone like me gone way too far?

After all, wouldn't I love nothing more than to pet a wild grizzly, to have it smell my hand, to sit a few feet from cubs? To camp next to a fox den? Any wildlife interaction I LOVE. But, I am too careful, and too worried about the long term effects on the animals. I never feed wild animals as they can't afford to become dependent on humans. I try NOT to habituate them and to maintain a respectful distance at all times. But, my actions always fight against my desires to get close. I think Treadwell was a special kind of crazy - a lot of which I can actually see or feel shadows of if I try. Some aspects of him - his extreme depression, paranoia, addiction, egotism, I can't relate to at all, but his way of soothing himself - getting lost in nature, I completely get.

I don't know that Animal Planet should show the tapes he made, but the footage IS amazing, and the stories are good. You just have to keep in mind - he was nuts. He paid the ultimate price, and what would have been saddest of all to him was they killed the bear that ate him. He would not have wanted that. He truly would have been okay with the bear continuing to live. And I get that too. When you put yourself out there in nature, if it gets you, it's your own fault.

Thursday, September 4, 2008

Bob the Euglena, and Back to Biology

Click here for a picture of a Euglena, a greenish single celled organism that moves around via a little flagella. I was looking at these live and up close via microscope this week as part of a Biology class I started taking. I decided to go back to college after all this time and get another degree, in Biology, if I can swing the hard math and science classes that I avoided during my first trip through college for my B.A. degree.

This time is all sorts of different. Since I already have degrees and a job, there are a lot fewer unknowns. I am older so my experience and approach to school is different. It's been 20 years since I had high school bio or chemistry, so I am rusty rather than freshly tuned up on those subjects. The field has changed a lot in the last 20 years too. The school is totally different than where I did my undergrad. Textbooks are different - they have interactive online components. Registration is different - everything is online, even paying tuition. Living off campus and being a married adult also makes for a different social scene than that present at my tiny, on-campus only liberal arts college in the nineties.

The biggest difference I am struggling with is that my study techniques which were tried and true for my undergrad and graduate school are not well suited to science, and I am having to adapt those. I also hate the fact I am not allowed to throttle people in the lab who move the slides, bump into the microscope, bump into me while I am looking in the microscope, and generally create chaos as we are racing around to prepare, view and draw 10 slides in 45 minutes or some equally impossible task. My patience for such things is less than when I was younger. My eyesight is also poorer, so while I am not yet 40, it makes me feel in my '50's. I am struggling to make my study time effective and minimize it so I am not spending sooooooo much time on this one class each week.

So back to Bob....or rather, that is what I named the Euglena I spent the most time looking at. They were all so cute. They all swam really fast under the microscope and passed in and out of view. Then we added some "quieting solution" and the swimming slowed down. Bob was industrious though, and way more beautiful than any image I could locate on the web. The light lit up his little organelles and other contents beautifully. His movements were graceful. I was very distressed that the end result for Bob and his buddies was getting washed down the drain. Truly, life even in that simple form is really neat to watch and I have to admire it - not want to destroy it, particularly because it seems to me we could either destroy one slide per lab instead of 10, or maybe even let them live and reproduce in peace, just wash them back into a jar. Why the needless single cell deaths?? Sigh. That's a bit hard to take, but the subject matter is still really interesting, as I remember it was all those long years ago now.

Wednesday, September 3, 2008

Palin Supports Aerial Hunting - Yuk

I was aware that Sarah Palin supported aerial hunting of bears and wolves in Alaska, but not fully aware of the extent. The more I read about her, the less I like her. Defenders of Wildlife put out this little video to help let people know where she stands on that issue. I doubt too many people will care since aerial gunning is not a hot button issue for a lot of voters this election, but still. What does it say about someone that even this unfair method of hunting, which can be totally brutal, is okay (I mean really, do we have to find them from the air and run them to exhaustion - how can anyone say that is good sportsmanship). I would hope that even most hunters would be willing to draw the line before condoning aerial gunning. If you can stomach the footage (which is hard to watch) then here is the Defenders piece:

Monday, September 1, 2008

Which Candidate Is Best for the Animals?

The big issues affecting animals: environmental conservation, endangered species protection, climate control/global warming, and factory farming. While I'm sure there are others, those are the biggies right now. While I realize I am in the minority, those issues are more important to me than the economy, or social issues.

The environment is an easy one. Obama is clearly better on environmental issues than McCain, based on their voting records in the Senate, not just their campaign rhetoric. Biden's voting record on these issues is also very good. The Sierra Club and other environmental groups endorse Obama and Biden for this reason, and compile voting records which you can search for to see the "report cards" on the issues, which you can then verify on the Senate website if you so choose. I might note also that Palin is horrible when it comes to environmental issues, to the extent she has a record on them. She is hard core "old school Republican" and believes humans come first at all costs. (If we need oil, drill in the wildlife refuge, no question, etc.)

Obama's ticket also wins on endangered species protection. Palin is a particularly bad pick for McCain when it comes to this issue, as she initiated an action against the federal government to prevent endangered species protection for the polar bear. Despite all the science and hard evidence to the contrary, and even the Bush Administration's agreement to give the polar bear endangered species protection, she believes they are doing just fine. She is adamantly opposed to their protection. Here's just one article highlighting her polar bear stance, but a web search will give you many more, including video clips on YouTube of her TV interviews. At least equally appalling, if not more so, is her support for aerial gunning ("hunting") of wolves in Alaska. She not only supports aerial hunting, but she has worked with the Alaska legislature to try and prevent the citizens from having a direct vote on the issue. (Alaska once voted to ban such hunting, which was overturned by the legislature).

Obama/Biden are also clear choices on energy issues and global warming, recognizing that there is urgency in addressing those issues for the sake of the planet. McCain, not so much. Though he claims to support these ideas, his actions and voting record do not support his rhetoric.

Here's a summary of some of Biden's views on energy and science issues, including climate control, from a group called Scientists and Engineers for America. Here is Obama's from the same group. McCain declined to answer their questions but they compiled information on his science related positions here. I might note that not answering is consistent with McCain's attempt to do only what is good for his campaign...answering questions nails you down and can cost you votes, while leaving things open creates ambiguity and maybe you'll keep some votes because voters make assumptions about you.

Particularly disturbing to me is McCain's taking this attitude all the way in failing to show up and vote on key alternative energy legislation. He was in DC when a key vote was taken but failed to show up, and so the measure failed by one vote. (Obama was present and voted for the bill). McCain had a chance to do what was good for America and support wind power and alternative energy but he took the easy way out and supported the oil industry by failing to appear - he would have made the difference. He did what was good for the campaign - remaining ambiguous - as he can now claim he supports alternative energy despite his abysmal lack of ever doing so on the Senate floor when it actually counted. He has actually missed EVERY energy vote on the Senate floor, more than 11 in all. His talking points are just that - his action is to not show up, not cast votes that matter, and not get serious about energy policy in a meaningful way.

Palin is another example of a choice me made that is good for the campaign and not the country. Seriously, he could hardly have found a less qualified candidate, and for someone 72 to not put the best interests of the country ahead of trying to win the campaign is pretty repugnant. I know he wants to pick up the religious right and since she is exceedingly religious and has positions in line with the hard right she helps him do that - but it undercuts any moderate stance he might have been trying to pull off.

As for factory farming, neither candidate has chosen to make statements about seriously changing this. Obama did at least bother to respond to questions about it, and while I don't particularly like his failure in his response to address humane conditions for animals, at least he responded. As usual, McCain didn't. Had he, the typical Republican platform is to support CAFOs and justify factory farming conditions with responses about the economy and ignore the animal issues. However, he would like to leave this too ambiguous, it appears.

While I have never considered myself a Democrat, I have to say that this election I clearly can't support McCain, even without the hideous addition of Palin. While Obama has not expressed the concern for animals I would like in a candidate, I understand the political reality that he has to address the issues that concern most people, not the fringe issues. Sadly, animal conditions remain a fringe issue at this time. But, at least he bothered to respond to questions, and on the big environmental issues he is definately a strong choice.

It will be an exciting election. I do think it's a great sign that finally both parties had a moderate candidate instead of the extremes that usually come out of primaries. Can you imagine a race of extremes with Hilary Clinton v. Mitt Romney? We'd want to kill ourselves with choices like that. At least this way, we have two relatively moderate choices. Unfortunately, McCain is swinging to the right, and Palin particularly skews things hard right. If more people participate in primaries, we can select less hard core extreme candidates, a step in the right direction.

Now we sit back and wait to see how it all plays out.