Wednesday, September 17, 2008

In transit

I'm moving to Wordpress for some new tools. Please update your bookmarks.
I have a post already up on glossolalia; it's fun.

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Tuesday, September 9, 2008

LHC!

Well, the LHC will go hot tomorrow! You can watch it live here:
Live webcast
Now for some fun updates
First (.Y.)
Sorry, I had to, but seriously POOR PENGUIN!
This too
And this
Also this
And finally:

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Very funny video

So, I've found this video on youtube showing the "amazing" things they're doing have been researched?
For the "speaking in tongues" thing:
"In 2006, at the University of Pennsylvania, researchers, under the direction of Andrew Newberg, MD, completed the world’s first brain-scan study of a group of individuals while they were speaking in tongues. The study concluded that while participants were exercising glossolalia, activity in the language centers of the brain actually decreased, while activity in the emotional centers of the brain increased. During this study, researchers observed significant cerebral blood flow changes among individuals while exercising glossolalia, concluding that the observed changes were consistent with some of the described aspects of glossolalia. Further, the researchers observed no changes in any language areas, suggesting that glossolalia is not associated with usual language function."
Just watch, you too will be on the floor, perhaps from laughter!

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Friday, September 5, 2008

Gustav Progress Report

Part 1: New Orleans isn't all there is in Louisiana!
I have a bit of a rant. Most people I've spoken with seem to think the hurricane wasn't that bad because New Orleans is fine. Au contraire! Here's a map of who is without power CURRENTLY in Louisiana that are normally supplied by Entergy. This is five days without power, some of them still aren't allowed back to their homes (Terrebonne parish) and some aren't expected to get power until October 1st (Donaldsonville). In the event you are one of the few that considers New Orleans the only major city in Louisiana, perhaps I can put it into perspective. Peak power outages for the state of Louisiana provided by Entergy numbered around 1 million. Other companies (SLEMCO and CLECO) also had many power outages (100,000 and 200,000 respectively). So this means that in total, almost 1.3 million people were affected. Of the 1.3 million affected, just over 500,000 are still without power. That's more than the number affected by Katrina in Louisiana STILL WITHOUT POWER FIVE DAYS LATER! Katrina caused 400,000 power outages in Louisiana; 1.3 million outages in Florida. So, if you think Katrina was bad for us, let's put some perspective on things.
Part 2: Government response
Whatever dumbasses are trying to spin this as an effective government response can kiss my white ass. While it is certainly far better than what it was after Katrina, I must explain my point. The city services are still nonexistent in Baton Rouge, Lafayette has just gotten some services back. Many cities still have very little water pressure due to a lack of fuel for generators which supply water. Food and drinking water take hours of waiting in line to get and they request that you don't park and block other vehicles. This means that you burn more fuel sitting there doing NOTHING waiting while the National Guard loads up people in front of you. Fuel takes hours of waiting in line (so you burn a tank of fuel waiting to get a tank of fuel) to get because only a few gas stations have generators to pump gas. Trees are still down across many streets!
Part 3: What worked
The Red Cross gets major points from me on this one, they have been doing wonders handing out food and water. Far better, I might add, than the agencies assigned EXCLUSIVELY to do that. You know this agency, FEMA, supposed to stand for "Federal Emergency Management Agency," I think it stands for "forget expecting meaningful answers" or "find external means of assistance." I think this FEMA would do a better job. Those asshats couldn't manage an emergency shit, they just watch. They botched Katrina which lead to deaths, they're botching this one which is only going to result in many people suffering without any means of cooking, bathing, or keeping cool in the wonderfully hot Louisiana summer. At least some organizations have been doing decently in helping out Louisiana. Have I mentioned the Red Cross is awesome? Seriously, donate to them, or at least volunteer for a weekend, donate blood, something. Lamar also donating tarps and using their electronic signs to post emergency messages. Major kudos to them.
Part 4: Midterm grades!
Since we're still lagging on the recovery effort in many places, I can't call this a final grade just yet, but it's not looking good for some, others, it looks pretty good.
Electric companies: 50% overall (scaled by customers)
Slemco: 85% B Took them a few days to get most people up and running, but they had some serious damage to their lines that I saw, most of the pictures of downed lines are Slemco lines.
Cleco: 70% C They still have some work to do, but they're not doing too poorly
Entergy: 40% F For a major electrical company with hundreds of repair crews and hundreds more crews from around the country here to help, they can't manage to get power to more than 50% of their customers in 5 days? Seriously, 5 days is way too long for anyone to be without a means of cooking, bathing, or keeping cool. At 75%, people stand a pretty good chance of having friends with electricity where they can go, but at 50%, it's unlikely.

Government: 60% D-- They completely failed for Katrina, this response may not result in as many deaths from governmental lack of response.

Private companies: 90% A These companies aren't required to help, but many of them that are capable of helping are doing so. For that, we greatly appreciate it. Thanks.

Police and National Guard: 70% C Not a complete failure, but some of the representatives of these agencies could be a bit more assistant when it comes to problems. For example, closing down one of the few fuel stations because the lines were blocking traffic DOES NOT HELP MATTERS! All this does is shift the lines to other fuel stations which ALREADY have similar lines, so you are making it worse. Not only that, the individuals which were sent to close said fuel station were quite rude and unhelpful.

I spent the better part of 4 days cleaning yards, cutting trees, and helping family, tomorrow, I go to help my girlfriend who is also one of the people without power.

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Time for an experiment!

You know, I was reading a comic and came across a pretty cool idea for an experiment, I was just wondering how I could possibly get funding and lab space to do it. It's after the fold...



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Wednesday, September 3, 2008

The best of the worst!


This was right before the eye passed over us, the winds were starting to die down and the rain pretty much stopped. You can see how flooded the field across the street is.

This is where I watched the heaviest part of the storm from, you can see limbs down and the flooding here as well.

The ground was so saturated that by the time the eye passed us, when I walked outside, I sunk ankle deep in mud. That is why the video I posted previously was on the north side of the house, I didn't sink when I tried walking out, although the other side had a much better view of the other side of the eye wall.

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More pictures


This is what happens to a van when a transformer falls on it.

Here's a partial view of a house with a tree ALMOST on top of it, you may not be able to tell, but that tree is being suspended by power lines.
I somehow don't think that fence did much good keeping the trees out of the house...

This is the front of the local high school (which had a collapse due to structural failure).

This gas station has the roof of the awning removed completely.


BIG tree knocked over, I think it was hit by lightning prior to this storm, though.

Trees block many of the side streets...

Power lines running across the yard, and a tree almost fell on this house.

This is that same house with another two trees nearly missing again.


I don't think anyone will be going in or out of that driveway any time soon.

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Hurricane damage photos!


In case you can't really tell, all four of that car's tires are off the ground.

This is part of the reason why power is out over most of south Louisiana.

Here's another part of the reason.

Since power is out, lots of people with generators need fuel... and most fuel stations can't pump fuel because THEY don't have generators, so the few that do look like this (we found two fuel stations with gas).

This store had the top peeled off much like a sardine can. I guess the employees finally have that sunroof they wanted...

This just illustrates how strong the winds were, that sign is supposed to be vertical....

That WAS a Taco Bell sign. Also, wind wasn't coming directly at this sign, it was flowing from left to right and then from right to left.

Another telephone pole snapped like a toothpick.

One of the numerous uprooted trees.

video
A short little clip from the eye!
Going take more pictures now, back later.

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Monday, September 1, 2008

I'm back!

The worst has passed, I will probably be able to post pictures tonight

This mobile text message is brought to you by Jared!

UPDATE 9/3/08: I hate AT&T for affixing an advertisement on a text message that I pay for, fucking bastards. Anyway, I'm alive, I have internet, so my next post will be photos, lots of them!


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Blogging by cell phone!

It seems we're getting 75 mph gusts with 60 sustained. Flooding.

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Monday afternoon

1:00 PM
I'm now going to give you a vicarious experience of a hurricane which is unlike what you see on the news, be prepared!

These two trees will probably be permanently bent after this, winds are constant at around 35 mph with gusts in excess of 70 mph.

The hurricane is currently 60 miles to my southeast moving at 14 mph northwest. Current winds are around 105 mph. It's anticipated to be directly over us by 8:00 PM Central Time. I'll be taking photos throughout, but pending internet, they may not be uploaded.

If I still have internet at that time, I'll be posting pictures, otherwise, I'll be writing up a report to post when I do get internet again.
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1:15
Winds picked up again, constant speed is near 40 mph with frequent gusts to 70 and occasional gusts near 80.
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1:25
Well, sustained winds are going to be climbing rather rapidly, my girlfriend just sent me a photo which I will be uploading shortly. She said her sustained winds are in the 80 mph range. We're now in the 50+ range and it will reach 70+ mph sustained in the next 3 hours.
Here's here photo

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Monday morning...


7:40
Well, I'm awake, we keep getting these little bursts of rain and a steady wind of 20 mph is blowing from the northeast. The forecast has it ranging from passing directly over us to not even making landfall. All of the models take it directly over us, though. The clouds are moving considerably faster than they were yesterday and the hurricane is projected for landfall in about four or five hours. A few of the frogs from last night are still out and seven small birds, not sure of the species, are sitting on the powerline. The birds were flying into the wind from the south, they didn't really have much in the way of ground speed...
Winds are gusting to about 30 mph pretty frequently.
I'm going to see if I can't get any good pictures.
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8:35
Winds are gusting to 30 mph with a constant 22 mph breeze. It feels really nice outside, not too hot, nice wind, it's fairly pleasant with the exception of the sense of impending doom...
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8:55
Clouds are moving pretty rapidly across the sky, not sure at what speed ,but they traverse from directly above me to at 45 degrees in a little under 2 minutes. It's somewhat creepy.
Anyway, the reason I started this post is to bitch and moan about the news agencies constantly talking about "how bad Katrina was" and "how long it took to recover from Katrina." These folks haven't a clue. The parts of New Orleans that you would actually want to go to were fine within a year after that particular storm. What made Katrina so bad wasn't the storm itself, it was the stupidity of our leadership. Thankfully they learned from their mistakes, but that doesn't mean these leaders are intelligent, just means they don't want to commit political suicide. One news guy said that "Baton Rouge will be fine if the levees hold"---WHAT THE FUCK!?!?! The levees of Baton Rouge are for the Mississippi River; now, in the event you are not familiar with storm surge, rainfall, and the size of the river, let me explain why that was a retarded statement.
1) Nearly all of Baton Rouge is located above the water level of the river
2) The only way for the river levees to overtop would require massive amounts of rainfall
3) The levees in New Orleans broke because the water level from the storm surge was way above normal and water began flowing over the top and eroding the dirt on the back side.
4) The Mississippi River in Baton Rouge can be 15 feet above normal and still have ample room to rise.
5) The levee that broke in New Orleans was for a canal, not the river.

OK, enough of my rant, now for photos



_________________________________________________
10:15 AM
We're now in the first arms of the hurricane. it's not too bad yet, raining at rate of 1/2 inch per hour, but climbing. Winds are sustained at 25 mph with gusts to 35 mph and higher. All of the computer models have the center of the eye passing 10 miles south of me in 10 hours, which means we will get the weather to the north and east (the worst parts of the storm). It's also beginning to slow, it's currently only moving at 14 mph as opposed to the 19 mph it was moving yesterday.
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11:25
My girlfriend just called to tell me she lost power and they'll be starting up the generator soon (that's one of the generators I set up). She's just south of Baton Rouge. She was going to send me pictures as well, but I suppose I'll have to put them up later. In any event, it's still raining at about the same rate, winds have picked up slightly and the clouds are moving slightly faster. The frogs are still safely tucked into the corners on the porch and no trees have turned into javelins yet. Current relative position of the eye of the storm is due 40 miles south of Baton Rouge which is 60 miles to my east. This means the storm is about 70 miles southeast of me and moving towards me at 14 mph. This means 2 hours or so until it begins getting really nasty.
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My location is centered on this map.
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Sunday, August 31, 2008

New Hurricane Post

Since the other one was getting a bit long, I figured I'd continue it on a new post. I'm sitting out on the front porch at the moment, which faces West (so I can actually be here throughout the storm if I so choose) and enjoying the very quite night air. The air has this quality about it, kind of like being in a steam room that's just slightly cooler than it should be, but there is a light breeze (5 mph or so) and I'm with my froggy friends that I mentioned earlier. I'm kind of hoping for more wind and rain soon so the vampire bats mosquitos go away. I think one the size of a hummingbird just flew by.

The worst part about hurricanes, in my opinion, is the anticipation. It's like the anticipation of surgery, you know you'll hurt for a few days, but you don't know exactly how long it will take to recover or if there will be complications.

To prevent being carried away by vultures mosquitos, I'm going to adjourn to the interior rooms with air conditioning until the winds pick up a bit, may as well charge up the computer while I'm in there, too.

I just remembered, I wanted to extend my thanks to my Hyla friends next to me preventing mosquitos from making me require a transfusion. I'm O+ in case anyone was wondering...

Next update will be when the rain comes again....
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10:08 PM CST-it's still Sunday
Well, it looks like we won't be getting anything for a few hours, so I'm going to take a nap and charge my computer...
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10:23 PM
I overheard the radio with Archbishop Hughes of New Orleans saying he was "praying for the least damage." I wonder if he realizes that the "least damage" may involve the hurricane taking a path over people that are less prepared than we are here at the moment. It's a damn good thing prayers don't work...
Oh yea, anyone else think it's funny how this hurricane hits during th Republican convention instead of the Democrat convention like this guy wanted. Just another example of the power of prayer [to fail].
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11:05 PM
Well, I managed to get teh interwebs indoors here, so that means no mosquitos, less humidity, and A/C! I'm keeping an eye on rain bands, and I intend to take video of the heavy stuff if it comes this way. My girlfriend recently told me she'll be taking pictures and e-mailing them to me. She is located about 70 miles East-southeast of me.
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Hurricane updates

Well, I took some pictures of the lovely weather we have now, I'll try to add photos from the entire duration of the hurricane, pending power and internet connection. So here's what it looks like now in Opelousas, LA.
Sunday, August 31, 2008 at 12:00 CST
Images 1, 2, 3

The last two are actually not duplicates, I took two in rapid succession to illustrate a lack of wind right now; I'll probably refer to these later.
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Clouds are beginning to roll in at 3:00 CST...same place

More and more clouds, a light breeze, but overall, it's fairly warm and pleasant outside at the moment...
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Well, the hurricane sped up a bit, now moving at 18 mph (29 km/h) so that means it may pass over slightly faster. This is a good thing. Most people always thing wind causes the most damage, but in reality, the ultimate causation is the rain. In Louisiana, we have very, very rich, soft, soil that can hold quite a bit of moisture, but once it reaches the saturation point, it doesn't take much wind to uproot a tree or shift a building's foundation. If you look at the pictures from downed trees after Katrina, you'll notice most of them still have the root structure intact. This indicates the ground was saturated and soft. Most of the trees that are actually standing in Louisiana have been through a hurricane or two, so wind really won't uproot them, they tend to have a solid root structure. Saturated soil is what makes it possible for trees to be completely uprooted. Anyway, these two images give you an idea of where I am.

It's going to be an interesting night...
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Not much going on, we relocated to a safer location: brick vs. wood. More photos pending unpacking my camera again.
Looks like I'll have internet unless the power goes out, YAY!
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6:30-took some pictures, here's some of the clouds coming

1720-rain coming, I can see a band off in the distance, not going to be one of the bad bands just yet...

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7:35, just started raining, the sun's still out, I'll post the picture later.

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Hyla squirella! There are hundreds of these things under the front porch where I am currently located sucking up bandwidth from the neighbor (he's a friend of mine). I absolutely love it. The sounds are so amazing.
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8:46 PM, still Sunday
First major band expected to hit here around 10:00 PM
Next post will be froggy pictures!
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Saturday, August 30, 2008

Gustav is on his way...

Well, it seems that hurricane season is upon us, and here comes one two three tropical storm storms... I just finished prepping generators for three houses, cleaning up projectiles wood in the yard, and checking food stocks. Let's hope New Orleans doesn't get trashed again, I like the French Quarter...
Those of you in the Gulf South (I know I get hits from Louisiana, Texas, Florida), good luck to you.

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Friday, August 29, 2008

Obligatory political post...

Well, the results are in, let's find something good to bash every candidate for, below are the list of each candidate and why I think they are complete morons:
McCain: Opposes abortion, favors "equal opportunity," favors abstinence-only education, and favors vouchers for education.
These are all bad ideas because:
1) A fetus is not a human, in no way, shape, or form has any compelling argument been made to suggest that a fetus has the ability to think or feel. In fact, the destruction of a fetus or embryo is less the destruction of a human than cutting off your own hand.
2) Affirmative action or "equal opportunity" presents the problem of benefiting upper class minorities far more than the lower class, the very people it is supposed to help.
3) Abstinence only education fails.
4) Vouchers leave only the poorly performing students.

Next person: Obama, I'm going to truly be fair and explain why I think this guy is an utter numbnut and politician. He actually decided to answer the Science Debate 2008 questions, and for that, I applaud him, but he answered them in a completely indirect way dodging most of them and only giving, what I like to call, "post-modernism answers." There are no answers here, they only raise questions. Here's a good example which I posted on ERV earlier...
As a resident cynic, I must say his answers are written similar to much of the post-modern literary criticisms I have read. A good example of this is:

" First, I have proposed programs that, taken together, will increase federal investment in the clean energy research, development, and deployment to $150 billion over ten years. This research will cover:"

Ok, let's see what research he's talking about...

"Basic research to develop alternative fuels and chemicals"

Well, that could be millions of possibilities, are they carbon-based alternative fuels such as biofuels or synthetic gasoline? Are these alternative fuels/chemicals including hydrogen? What about geothermal, hydroelectric, and tidal energy? This answers NOTHING, it just says "yea, I want to develop alternatives.." without saying anything about what they are. Next:

"Equipment and designs that can greatly reduce energy use in residential and commercial buildings – both new and existing"

Really now? I don't think a more vague statement exists, are there any specific technologies you have in mind or is this just another generic "oh yea, I'm thinking of something."

"New vehicle technologies capable of significantly reducing our oil consumption"

Doesn't this go with the "alternative fuels" group?

"Advanced energy storage and transmission that would greatly help the economics of new electric-generating technologies and plug-in hybrids"

Can't the previous two go together? And how would he "enhance" this research? It's ALREADY BEING DONE. Recent advances in Li-ion batteries, hydrogen fuel cells, and so forth are making it possible within the next 5 years to have a zero emission vehicles which are viable.

"Technologies for capturing and sequestering greenhouse gases produced by coal plants"

Which one? Also, CCS technology makes the plant require 25% more energy to operate thus meaning you actually use MORE hydrocarbons! Our problem isn't just CO2, it's also COST of hydrocarbon fuels.

"A new generation of nuclear electric technologies that address cost, safety, waste disposal, and proliferation risks"

Ok, which generation nuclear reactors? II? III? Invest in IV? Seriously, if you're going to make a claim as to what will happen, at least say HOW you plan on making it happen
I recently did a little quiz on On The Issues. My results were somewhat astonishing, I actually got a 45% agreement with one of them... Next up is candidate number 3, for this one we'll go on to the Socialist party. Brian Moore is also a complete fucktard and here's why:
Moore-on also supports school vouchers, doesn't want nuclear power, public ownership of all natural resources, and a $15/hr national minimum wage.
Here we go: school vouchers covered already, generation III and IV nuclear reactors are very safe and low on nuclear waste. Yucca Mountain makes a pretty safe place for storage. Top this off with research to develop fusion reactors after we've had nuclear, hydroelectric, geothermal, etc. power sources can aid us in providing some augmentation to a nuclear infrastructure. Public ownership of natural resources means "natural" resources such as trees, streams, and so on are all the domain of the public. Of course, he's also wanting corporations to be removed, but hey, he's a socialist...

Next up is Cynthia McKinney.
Do I really need to explain why I think the lady arguing a conspiracy theory and screaming "racism" every chance she gets is a complete waste of carbon, oxygen, nitrogen, sulfur, iron, and space. Perhaps we can toss her into a fusion reactor later...

After her, Bob Barr, Mr. Libertarian that thinks same sex marriages in one state shouldn't be required to be accepted by other states, but at the same time, he criticizes efforts to restrict rights of homosexuals. I don't know where he really stands on anything (or if he does) and those few things he does have a firm standing on I disagree with. Namely the "God Bless America" on schools and vouchers for private schools.

Now I'll move on to Alan Keyes and Chuck Baldwin: these two I can take out with one fell swoop; that is abortion rights. Both think abortion is equivalent to murder and embryonic stem cell research is bad. They are both very extreme in this with Keyes thinking "snowflake babies" shouldn't be experimented on either and Baldwin saying abortion is a holocaust. They also both like the idea of drilling in ANWR.

SOMEONE PLEASE FIND ME A DECENT CANDIDATE! Someone that could defeat this guy in a debate and possibly has IDEAS that MIGHT work.

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Monday, August 25, 2008

Fun with Creationists!

Well, some Creationist (not IDiot, the regular idiot), posted a little snippet as a comment over on ERV. It's down at comment #6, but for easy of reading, I'll copy the entire thing here...

We fully expect you to NOT post this, but we'll give it a whirl anyway.

Please refer to:
http://www.whoisyourcreator.com/endogenous_retroviruses.html

Do they expect it not to be posted because it is complete nonsense? I certainly think that's why it wouldn't be posted...

More below the fold...



Scroll to:
"How is it that ERVS are Considered Copies of Disease Producing Exogenous Retroviruses but None Have Been Proven to Directly Cause Disease?"
Ok, it's complete fiction; in the event you are unfamiliar with multiple sclerosis, I suggest reading up on it. Also, we would expect HERVs to lose functionality if those humans are to survive, if they are completely functional and cause disease, person dies, ERV goes away.

"By Chance, What Made ERVS Evolve into "The Cure," Instead of Remaining Disease Related Viruses?"
As stated previously, ERVs with (notice the last "s" is in lower case?) beneficial effects are kept, those with extremely deleterious or no effects undergo much more mutation.

"By Chance, What Made ERV Elements Change From Viral Activities to Cellular Activities and Create New Essential Genes?"
In the event you still don't get the effect selection plays on the survival of genes, perhaps you should take a few remedial courses in biology; ERVs seem to be far out of your league...

"ERVS Created the Specie-Specific Regulatory Network that Controls the Expression of Cells in a Collective Manner. What Came First � the Host or the Regulatory Network?"
This is a false dichotomy; neither came first, retrovirus invades germ cell-->germ cell produces gamete-->infected gamete forms zygote which grows up to be adult (if virus doesn't kill it)-->virus loses some functionality due to mutations-->genome adapts to include ERV as functional element or ERV slowly disappears... I know, that's really simplified, but I figured I wouldn't make your brain explode just yet...

"By Chance, What Made ERV LTRS Immediately Turn into Essential Gene Regulators Upon Insertion?"
In the event you don't know what an LTR is, it is a "Long terminal repeat" which is used for insertion into the host DNA; now, what happens is after dsDNA is formed, LTR-specific integrases put the DNA into the genome. Now, they are presenting evidence that the TF binding site was present in the consensus sequence of the original retrovirus, it didn't "turn into" anything, it just happened to contain the consensus sequence for the TF in the original consensus sequence of the retroviral integrase because it is present in many related species... no magic...

"By Chance, What Made LTRS Gain Transciptional Abilities for Essential Genes?"
As the lovely lady over at ERV already said, "Its possible that a retrovirus plops down next to a gene, and the genes like 'Whoa! Ur a better promoter! I keepsies you!!'" Neat, huh?

"Misc. Examples of biased and inaccurate research and publications:"

I could explain each and every one of these papers, but then how would you learn?

Please note that there are about 50 + research articles referenced so we look forward to your rebuttal.

(If you can restrain yourself, it would serve all of us well if you would debate without insults and foul language.)

Posted by: who is your creator | August 25, 2008 4:52 PM

Look, I went the whole time without using any words you may consider "foul."

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Beauty Pageants and Habits?

No, it's not what you think! Nuns aren't protesting beauty pageants as "amoral" or "in poor taste." An Italian priest by the name of Antonio Rungi is holding a beauty pageant for nuns...

Next for news, and this is slightly more serious, teaching science to high school students that are brainwashed into being bible-carrying creationists has a new hero.
More after the fold...

And now for a little Swedish humor, I think my lovely Swedish girlfriend will enjoy it...
And more Swedish humor....

And here's one along similar lines. Isn't it any wonder how the ugly women are generally the ones saying looking at beautiful women lustfully is bad?


Finally, another awesome blog to enter into my blogroll! Cognitive Daily

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Sunday, August 24, 2008

Cancer 101-The End

Cancer--Next two papers!
Again, you should see my previous posts (here and here) on angiogenesis.
I'm going to summarize these two (here and here) papers in one (hopefully) short(ish) post and wrap up angiogenesis discussions for a while. After this, I will go into something far more fun; I've got lots of fun things in store!

So here we go:
I'm going to start out with a little info on CXCL4, also known as PF4. CXCL4 is fairly small, only 70 residues, and looks something like this.

It binds to several integrins (αvβ3, αvβ5, and α5β1) and by these integrin interactions, inhibits angiogenesis to some degree. Unlike HB-19, CXCL4 does not invade the cell, but functions as a surface signal. CXCL4 blocks endothelial cell migration in response to VEGF and FGF, and as a result, prevents angiogenesis. The precise mechanism of this is not yet known.

It is also interesting to note exactly how many things
αvβ3 actually binds to, I may make a post on this in the future, but I'm confident that, if you are interested, you can find many of them.

Lastly: Erythropoietin (EPO) blockade; not the same as a naval blockade, but similar

Recombinant EPO therapy is commonly used after chemotherapy to replenish red blood cells. This has been implicated in making recurrence of tumors far more likely. These researchers decided to look at what EPO actually does with regard to tumors and angiogenesis and the results were pretty interesting.

Studies previously looked at systemic and short term EPO treatments to determine effects of EPO on turmors while this study involved high concentrations of EPO in the tumor microenvironment.
Now, this is interesting, but doesn't really give any good treatment options. It does do something, however. It tells us how NOT to treat after chemotherapy. We should NOT give high doses of rEPO to patients after receiving radiation or chemo.

I'm going to conclude here by saying these three papers I covered (two of them only very briefly) are part of the rapidly growing body of knowledge relating to cancer formation, growth, and progression which will ultimately lead to our ability to treat most, if not all, forms of this disease from humans, and perhaps pets as well.

Here is a little hint of what is to come:
WMD
Naturopathy quacks

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Atheist Antarctica Escape

Here's an image of a rough little idea I had as a response to Tom Willis, one of the crazy creationist morons I am familiar with. PZ Myers bought this recent little tidbit to my attention, so I figured I'd make a little image of what I thought such an "evolutionist colony" should look like. It comes complete to be self-sufficient in terms of power, food, education, etc.
Ready for it?
It's after the fold...





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Saturday, August 23, 2008

AWESOME!

Flip over to Hyphoid Logic, he put up a neat little blurb on Fleshmap.

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Friday, August 22, 2008

Funny picture


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Cancer 101-HB-19

I'm going to start with this paper.
But if you haven't read the intro yet, and you don't know much about cancer, you probably should start here.

Nucleolin is a potential target for tumor treatment for a number of reasons. Chief among these is the fact that nucleolin plays a role in angiogenesis, and as previously stated, without angiogenesis or metastasis, tumors cannot exceed a very small size. The researchers here used an antagonist to cell surface nucleolin (HB-19 and anti-nucleolin monoclonal antibody (mAb) which, while not resulting in disruption of normal cell metabolism and behavior, resulted in marked decreases in tumor proliferation. Another observation was that a marked decrease in cells at S phase was observed. This is consistent with the expected decrease in replication of cells via prevention of DNA replication.

Now for angiogenesis. The researchers then looked at VEGF stimulated HUVECs ("vascular endothelial growth factor" and "human umbilical vein endothelial cells" respectively) . When VEGF or PTN (pleiotrophin) were used, HB-19 and anti-nucleolin mAb had very similar inhibition of vascular formation. When FGF-2 (basic fibroblastic growth factor) was used, HB-19 had a much higher efficacy than anti-nucleolin mAb at decreasing angiogenesis.

They then had some fun torturing poor little athymic nude mice. They injected human breast carcinoma cells (that proliferate when untreated into palpable tumors in two weeks) into them. Following this, they began treatment with tamoxifen in some mice and HB-19 in others. Autopsy revealed no side apparent side effects compared to control mice injected with phosphate buffer solution (PBS) alone. The HB-19 treated mice also exhibited no side effects such as diarrhea, infection, weakness, lethargy, blood cell counts, or body weight. Mice treated with HB-19 also exhitibted some elimination of measurable tumors. HB-19 was also more efficient at treating tumors than tamoxifen in higher dose levels! Now, HB-19 was not as effective as 5-FU, however 5-FU has significant side effects on lymphocyte counts.

So, what does this mean? Well, firstly, HB-19 may make a very good auxiliary treatment for tumors. It may allow chemotherapy to be in much lower doses and far less frequently. This is one possible route for tumor treatment presented by this specific research. The other papers I'll be talking about will further explore ways to control and treat angiogenesis and thus, tumors.

The final installment can be found here.

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Thursday, August 14, 2008

Cancer 101

We'll start out with a few definitions:
Integrin-cell surface proteins which interact with the extracellular matrix
Angiogenesis-the branching and growth of new blood vessels by growth of new branches.
CXC chemokine-small proteins (CXCL4 has 70 residues) which play a role in chemotaxis
Specific proteins to know:

αvβ3-vitronectin receptor

α5β1-fibronectin receptor; also plays a role in angiogenesis

CXCL4-an αvβ3 antagonist found in platelets and plays a role in neutralizing heparin like molecules thereby enhancing coagulation

Now for some basics on cancer.

As tumors grow, they require more and more nutrients to feed the mass of cells. To accomplish this, they rely upon angiogenic factors to trigger growth of new blood vessels bringing oxygen and nutrients. Metastasis is one way tumors spread. This involves the migration of a cancerous cell into the blood stream and moving to another location and invading the surrounding tissue further downstream by use of integrin proteins. By stopping cancer from producing blood vessels and spreading, we can isolate tumors to very small masses in isolated locations making them far easier to treat with very specific radiation levels in very specific locations.

But first, we must prevent metastasis and angiogenesis. I'll cover that next time.

Part 2
Part 3

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Upcoming and Response

I'm working on a post about CXCL-4, integrins, and cancer, but until I finish that, here's something I wanted to write to Mr. Ray Comfort, but I figured it would be overly long

Examples of species-to-species transitions are:
ring species of Ensatina salamanders
ring species of Larus gulls (kind of; it's really, really complicated)
[More after the fold]

These two examples are BETWEEN speciation by pretty much any biological definition of species. Neighboring populations can hybridize while distant populations cannot. You will rebut this by saying "but they're the same type." Yes, they are still salamanders or birds respectively, but, for example, are crocodiles reptiles? Myself, and many other biologists, say that while they are reptiles, they are a very unique kind of reptile with four-chambered hearts. This is very unlike any other reptile. It has also been established that genetically, crocodiles and turtles are slightly closer related to birds than other reptiles making the class Sauropsida paraphyletic unless you include Aves. Again, you'll say "common designer" but why, oh why, would a common designer include hundreds of sequences of transposons, retrotransposons, and silenced DNA sequences not present in the genetic sequences of animals which are less similar? Your reply will be "we cannot know, because my God works in mysterious ways."

I'll even say to you that evolution DOES have problems, but the ones you are talking about are NOT the problems. By drawing attention to your nonsensical representation of evolutionary biology, the real questions are not addressed. These include:
1) classification of bacteria due to horizontal gene transfer
2) establishing phylogenies of asexual organisms
3) exploring genetic change based upon things such as codon bias and induced mutation.
4) Many others.
Note, these do not conflict with the current model, rather they are additions which need to be made. Most organisms DO evolve by natural selection and genetic drift. Viruses also evolve in this way, but they, and bacteria, are also much more capable of the aforementioned horizontal gene transfer. Viruses also are capable of introducing their own DNA, which is usually done via RNA converted into DNA then inserted into the genome, and thus giving us insight into said virus evolution, as well as the evolution of progeny of the previously infected organism.

Cue "cosmological evolution" argument which neither you nor I are qualified to argue. Unlike you, however, I have a collegiate education in evolutionary biology and have read more publications on genetics and molecular biology than you can pronounce the titles of (granted that may be zero); this makes me, while not inherently smarter, certainly better educated. You can start with Berkeley's kiddy version of an evolutionary biology course. Ernst Mayr's "This is Biology," Mark Ridley's "Evolution," and D.Q. McInerny's "Being Logical" also would be good reads for you.
*note, I could have included pictures and more links, but then you wouldn't have to do any work.

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Saturday, August 2, 2008

Evolve:Fangs

No, this is not another review of a show, not yet anyway. That will be on Tuesday. This is some speculation as to what selective pressures lead to the development of snake fangs. Researchers recently discovered how fangs develop and PZ Myers described the research in relatively easy-to-grasp terms. If you would like the original paper, the citation is at the bottom of PZ's review of it.

The paper addresses what we know about how snake fangs evolved, but it does not answer why snake fangs evolved. The selective pressures for snake fang development are fairly easy to identify in a stepwise manner.

1) no fangs, no venom
2) venom gland formation from modified secretory cells located in the mouth
I leave this one open for several purposes I shall get to later.
3) fang development (normal teeth being modified to form grooves)
4) in some species, the grooves were refined into hollow fangs, and in others, further evolution of the grooves occurred.

We do not, as yet, know how the venom glands specifically evolved, however, it is probable that some mutations prior to the separation of various lineages. Here's a phylogeny based upon mitochondrial DNA...below the fold.

If you look at the points of mutation among all genera containing venomous snakes (Viperidae, Elapidae, Colubridae, Atractaspis), all of them are related by a common ancestor dubbed Colubroidea. Dr. Brian Grieg Fry made a nice little breakdown of Colubroidea evolution.


It is likely that the evolution of venom glands directly lead to the development of fangs due to efficiency of delivery. The method of feeding for colubrid snakes is generally that of constriction with the venom serving the role of accelerating the death of the prey. It is also a misnomer that colubrid snakes are nonvenomous. Many colubrid snakes, in fact, have venom glands, but many are not harmful towards mice. Of the ~1400 species of colubrid, 700 have venom of some kind. This indicates that some species commonly classified as colubrids are actually closer related to other groups than previously thought. This is reflected in Dr. Fry's phylogeny.

It may also be noted that no snake species outside of Colubroidea has been observed to have venom indicating that venom production likely developed in one of the common ancestors of these organisms. I would also note that many of the proteins found in venom are made in many other parts of the body, so it could be a modification of the expression of these proteins which lead to the development of venom.

I would like to add that much of what I said is purely an educated guess as we do not have the data yet to prove it, but it does have evidence in the form of protein homology in a number of venom proteins for origins in other.

Now, for the glands. Because some species of lizards also have venom glands, it is probable that the development of a new oral gland much earlier than previously thought.

Since I find this so very interesting, I can go on at length about the the origin of the glands and how they form, blah, blah, blah. Instead, check out Dr. Fry's page, he's got lots of good information on there.

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