Where Is Joel?

So there has been a ton of hub bub lately over this article in “Trends in Ecology and Evolution”. The premise being that women make different mate choices while on their pill and while off of their pill. I read over it, and while quite interesting it seemed to ultimately be much ado about nothing. It just so happens to be an article easy to sensationalize by the media. I did learn something very interesting however that I had been up until this point unaware of with regards to women’s menstrual cycles and their sexual behaviour.

It has for a long time been understood that women are more attracted to men with high levels of testosterone during their most fertile periods and more likely to have a one night stand with these men, whereas during periods of low fertility women are attracted to men with low levels of testosterone and are more likely to establish a relationship with these men. Testosterone levels are evident when looking at men judging by their jaw line etc. and often their level of competitiveness. The assumption is of course is that during periods of extreme fertility women are attracted to high testosterone men because these men are most likely to confer upon their child the ability to survive while in low fertility periods women want low testosterone men as these men are more likely to stick around and care for said child. (The unfortunate implication here is that we possibly have an evolved tendency to cheat as cheating men and women both find ways of increasing the chance of perpetuating their genetic material… This is off topic however so I won’t delve into it any further.)

I had always assumed that high testosterone men were good genetic fathers as the male children would also inherit the high testosterone characteristic and be stronger and more capable of providing for himself. He would also of course be more likely to be selected to be the genetic father of the next generation, although there is no reason this behaviour would initially have been selected for before this trait existed. This paper presents the postulate that as testosterone is actually an immunosuppressant, being able to survive high testosterone levels are a good indication of genetic quality as the subject survives even with a weakened immune system. I’ve never heard this before and am going to have to think about it. It seems counterintuitive that women would want to pass a weakness like immunosuppression on to their male offspring even if that male offspring had a higher chance of genetic quality.

Thoughts??

Alzheimer’s. Apparently caused in part by the hyperphosphorylation of the human tau protein.

Well, every other single person in the world seems to be writing about this today, and why not, it’s pretty dang cool. As I don’t want to miss out on the action I might as well write a few things I think.

Ok, what the heck am I talking about? Ardi (Ardipithecus Ramidus) is the earliest pseudo complete skeleton of a homonid clearly related to humans. Yay!!! Why do we care??

For starters it’s not the missing link. Every time someone says missing link I feel like slapping them. I hate the term and think the whole concept of missing link is retarded. Evolution is a fluid process, of which there are huge chunks of gaps in the fossil record simply because there just aren’t *that* many fossils. There are always going to be holes in the evolutionary record of any species. The term was popularized in the 19th century and for some reason it’s like we just can’t let go. Even national geographic mentioned it in the title of it’s article on the publications.

Secondly, despite media already seeming to mangle this, it’s not entirely clear that this fossil is a direct ancestor to Homo Sapiens. It’s obviously not too far off of the evolutionary shoot so to speak and was at the very least likely very much like our early ancestors, but whether it was in fact my Great^200000 grandmother is a contentious issue that is likely to be debated for a very long time.

Now, on to what is dang cool about this guy (chika in fact.) Humans closest relative in the animal world is the chimpanzee. It has long been assumed that when we diverged from the chimp our ancestor was some sort of chimpanzee looking thing. The reason for this is that we feel like a superior species to the chimp, so evolution must have swept us forward while leaving them behind. (This is of course ludicrous, and no credible scientist would ever mention it, but you know you thought it!) We can tell when chimpanzees and humans diverged evolutionarily based on genetic evidence, we understand facts like how fast things mutate and we can determine the amount of genetic difference between the two species. Based on this genetic evidence it appears that humans and chimps likely diverged less than 5 and a half million years ago. (I’m sure I should add a reference here, but I don’t remember where I read that. Google scholar it, it was in Nature or Science I think.) Given that Ardi is 4.4 million years old our common ancestor probably looked like ardi.

The crazy thing is Ardi was a bipedal!! The crazy, slouchy, on their hand walk of chimpanzees likely evolved after we diverged!! The bipedal walk we treasure as being so distinctly human existed in a primitive form prior to divergence and then was evolved away in other species. Now *that* is surprising!! I’m sure there are about a billion other interesting other things about this discovery in the papers, but I’m lazy and this is the main thing that stood out to me. If it sounds interesting though go pick up a copy of science. It’s all very cool.

Lastly I’d like to point out that once again reasonable non-crazy people have fired another shot across the bow of creationism. Ardi is indeed a transitional form which creationists claim vehemently we have never found. Of course there have been other transitional forms found, but this one happens to be very high profile, so maybe when people here from a creationist that no transitional forms have ever been found they will realize that this is complete garbage. Of course the people listening to creationists probably don’t read all this whacko sciency crap that gets published in Science anyway. So maybe not.

Later!!

I wrote about this just a few short posts ago, how a species might evolve such that individuals made would make decisions that were bad for their chances of passing on their own genes such that the species would have a better chances of continuing it’s own genetic lineage. I mentioned this manifests itself in our own altruistic tendencies. It seems like someone else had the same idea.

I a recent paper on unicolonial ants (ants that form super colonies with multiple queens where the ants rear babies with little to no genetic resemblance to themselves.) Helanterä et. al. demonstrate this exact same principle and challenge the generally accepted theory that evolution functions purely on the level of the individual with our actions be designed to pass on the maximum amount of our own genome. (ie. if helping our brother have 10 babies makes us have one less that might be genetically advantageous to passing on our own genes.)

It’s nice to be validated.

While evolution is not a specific point that I do any sort of work on it is something that I am very interested in. From a genetic perspective the amount we understand with respect to evolution that we did not formerly understand is unbelievable. I find evolution particularly interesting interesting because it is so unfathomable timeframe wise as compared to our lives. It is a concept we imagine that we all understand, but it is so difficult to actually visualize the changes, particularly as someone who knows the involvement of mutation DNA repair and physiological changes.
That being the case there are evolutionary traits that are evolved in most species that seem very counter intuitive. The easiest example of this is the insane colorfulness of male ducks. As a less colourful duck a male duck could live longer, have sex with more hot woman ducks and have more little mini ducks on average. The situation would however not be sustainable as if all male ducks had the same behaviour there would no longer be any selectionary advantage. The issue is that evolutionary pressure is not just on an individual basis it is societal. Societies have not only a drive to continue to exist, but also heritable characteristics. For example behaviour is passed down both partially genetically and through instruction by parents.
One of the coolest examples of this is altruism in humans. Time and time again studies have shown that humans are intrinsically altruistic. The evolutionary problem with this is that throwing oneself in harms way to help another human is from an individual perspective a ridiculous decision. As a society however groups of people who do as such tend to survive better and so the societal evolutionary pressure overcomes the individual evolutionary pressure. Another cool example is wolves. A pack of wolves has only one set of cubs per year. If all the wolves just had sex all the time there would be way more cubs and each individual that was not the head of the pack would increase their chances of passing on their genetics to the next generation. The cubs however would not get the same attention, nor have as good of a chance to survive. Societal evolutionary pressure overcomes individual evolutionary pressure. Pretty cool.
I’m sure if I had not been drinking all day at barcampyeg I might have put this better, but I hope you all enjoyed.

JJ

As someone involved in biological research I get the opportunity to read lots of research in the field of biology.  (obvious right?)  The sad truth however is that the presentation of most papers is such that they are really dry!  Because of this *many*, but not all, interesting things I read come from Scientific American.  Today I read an article that was fairly interesting, but really makes me realize that biology and genetics as a science is still in it’s very infancy.

First a little background info for the not biologically inclined who wish to read this.  Proteins in out cells make *everything* happen.  When you move it’s proteins in your muscle cells.  When you eat the sugar is digested using proteins in your cells. etc.  So naturally when these proteins change so that they don’t work that’s bad.  The proteins are composed of amino acids and the order of these amino acids is essentially what makes a protein what it is.  The order of the amino acids depends on the gene that codes for the protein.  The genes are composed of nucleic acids and every three nucleic acids codes for an amino acid.  is.  GGC is Glutamine.  Hope that wasn’t too dense!

The catch is that there are 61 different combos of nucleic acids that can be used but only 20 amino acids, so sometimes and amino acid comes from more than one combo.  ie. GGC and GGA actually both make glutamine.  It has long been assumed that mutations in your DNA (ie. GGC->GGA) that do not cause a protein to change do not cause harm.  These are called silent mutations.  (Quick note for the biologically inclined:  Ok, we have long known they cause problems in bacteria etc.  but for various reasons they were thought to be benign in humans.)

Lastly, when human proteins are made, chunks called introns are taken out.  So the entire gene doesn’t actually participate in the protein.

Where is this going?  Simple.  As it turns out, among other things, the introns are determined by sequences of nucleic acids.  How obvious is that that the nucleic acid sequence should determine intron location?  Nucleic acid sequence determines everything else, like where to start making the protein etc.  The answer is it should have been obvious.  Despite the obviousness it took us until just the last 5 years to figure out that silent mutations can effect other things like intron location.  This after knowing for over a decade that for some “mysterious” reason it looked statistically probably that some genetic diseases are caused by silent mutations.

What’s the point of this?  Basically if this stunningly obvious discovery is new then what more obfuscated and difficult to discover processes still await our prying minds to unveil?  This is the reason it’s so exciting to work in bioinformatics.  The world is waiting for us to uncover it.  For discoveries such as this all the clues are there, but the amount of data is so vast that machine inference techniques need to be used to put it all together.  With any luck, I’ll be there doing it.  Up up and away.  (Or something else slightly more inspirational…)

I ran across an article yesterday about IKEA buying the right to name genes by funding cDNA research projects. The possibilities are hilarious. Maybe 5 years from now students will be studying cDNA sequence called KRAMFORS and BESTA. Really it’s probably just sunk money, no one will ever see this research but researchers. On the other hand if they find something important and name it after an IKEA product that really would be interesting marketing.

Considering perl is the language of bioinformatics it is ridiculous a quick google search did not return a module which has built in amino acid comparison matrices. I know, reading one in probably takes 10-15 minutes to write at most, but every 10 minutes people spend on soemthing that *SHOULD* already be done is a wasted 10 minutes.

Anyway, I might remedy this at some point, but should you plan on reading in the BLOSUM62 matrix here is a quick fix. Perl is not my fav language and I am no perl hackomotron, so I assume something about this is wrong, but it works. use at your own discretion and hopefully you found this in < 2 minutes. If I ever do choose to remedy this situation properly I will add an addendum to this post.

blosum62:
ACID A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1

readBlosum.pl:

use strict;

sub readBlosum{
open BLOSUM , "blosum62" or die "Unable to open inputFile.";
my $line = ;
my @acidIndices = split(/ /, $line);
my %blosumMatrix = ();

while () {
my($line) = $_;
my @scores = split(/ /, $line);
my $currAcid = $scores[0];
for ( my $i = 1; $i < scalar @scores; $i++) {
$blosumMatrix{$currAcid}{$acidIndices[$i]} = $scores[$i];
}
}

close BLOSUM;
return \%blosumMatrix;
}

my $blosumMat = &readBlosum();
print $blosumMat->{"Z"}->{"X"};


Also
a) Feel free to tell me what I am doing wrong, I always welcome an opportunity to actually learn this language with very little work.
b) How the F*** am I supposed to attach files to a blog post that aren't media files?? That would be very useful!

Lately being an environmentalist has been the cool thing. We drive our priuss (Not necessarily good for the environment btw), we compost, we serve organic products at our dinner parties, we ponder our carbon footprints etc. There are very obvious ways we are changing the world around us for example the temperature is increasing and free space for wildlife is decreasing. The world around us however is very complex an it’s impossible to guess all of the ways we might affect it.

One impressive such point was demonstrated by Burda et. al in the recent issue of PNAS. (I love being in school and having access to all of these things.) A year ago they demonstrated that when cattle and deer graze their herds organize to face the same direction along the earth’s magnetic field like gigantic bovine iron filings by your favorite magnet in grade 6. As it turns out this alignment breaks down near large power lines, cows near power lines line up at random. As the herd moves farther away from the power lines they once again organize. Our power lines through the wild actually change the direction animals face when they graze through altering the electric field! (I’m the first to admit, this amazes me. I always thought farmers who didn’t want power lines running over their fields were quacks.)

What we should ask ourselves is what does changing this behavior actually lead to? I have no idea, it doesn’t even make sense to me that an animal would evolve the desire to graze facing North-South. It does show us that we should carefully consider all of our actions and their consequences.