Fun for the biomedical graduate students

I know this is a few months old, but its still funny as shit. Also, huge kudos to the makers of this video.

How many aspects of "this bad project" can you relate to? My personal favorite is 'what's in this box?'

Explain Republican Economics to Me Again!?!?

Ok, so the republican dogma is that we need to cut taxes to...wait, actually we need to cut taxes on the ultra-wealthy, then we can finally balance the deficit and grow the economy and make Jesus happy. Now Im not an economist, and before you disregard anything that follows, please realize you aren't one either (unless of course you are).

One thing republicans do well (and probably democrats as well, but when do they ever stick up for their own actual policies as opposed to follow a diminished republican script?) is hit you fast and furious with a variety of different, slightly related, but distinctly different topics: Taxes, Job Creation, Deficit, Taxes, Unions, Balanced Budget, Taxes, ad nauseum. This serves to keep you disoriented by shifting from position to position and prevents them from having to deal with substantive rebuttals.

I want to deal with one rebuttal to the no taxes debate.

First some facts:
1. The rich are being taxed at levels not seen since just before the great depression (see figure). So, the rich who apparently are required to make the economy grow are taxed at levels much lower than at levels when the economy grew inordinately.

Source

You should probably realize that this graph does NOT include capital gains (buying and selling stock), which is at  15% (thanks for keeping that going Mr. Obama). If you make millions on the stock market, your tax burden is much less than those working for a living.

2. The tax rate is based on the level of income. So, if we say that the tax rate on people making $100,000 is 24% and the tax rate on people making $500,000 is 28%, then the tax rate on those making $500,000 is 24% for the first $100,000 and 28% for the remaining $400,000. I think most people in this country fail to grasp this point. WHAT!!! tax a $1,000,000 at 75%, that's unfair!!! Indeed, it is. But in the real world, not the one sold by pundits bought and paid for by the ultra-wealthy, the reality is different. here is the reality: If you made $1,000,000 last year and were single, the first $8,375 was taxed at 10%, then $8,376-34,000 at 15%, $34,001-82,400 25%, $82,401-171,850 28%, $171,851-373,650 at 33%, and $373,651-1,000,000 at 35%. But if you listen to the millionaire, it seems their entire income is taxed at 35% (which is about a historic low), but that's not true, actually its a lie. Only their income >$373,650 is taxed at that rate. (Of course any of their income resulting from stocks is only taxed at 15%, so if they make $500,000 from capital gains and $500,000 in income, which is $1,000,000 total; $500,000 is taxed at 15% and only (500,000-373,650 =) $126,350 is taxed at 35%.

Ok, so we need to make sure the rich keep more of their money (of which they have a tremendous amount, hence the nomenclature rich) in order to create jobs and balance the budget.

Create jobs: The idea is that if the rich have more money they will use it to start up companies and hire people. But that is not reality. The truly rich are conservative and hold on to their assets in bad economies. The poor/middle class spend their fucking money. If you give tax cuts to the poor/middle class, it goes immediately into the economy, not into gold investments. Poor/middle class people buy shit. Rich people do not (or do not need to, compare to the poor). Also, who the fuck thinks the rich are going to throw their money away on new businesses, when the poor/middle class are living paycheck to paycheck?  Supply and demand anyone? If there is little demand, why is Jane Q. Moneybucks going to start a company selling widgets when everyone is struggling to pay their fucking cable bill? In a poor economy, the money going into the riches' pockets, stays there, but in the poor/middle class it doesn't even stay in a pocket long enough to accumulate lint.

Balance the budget: There are two ways to balance a budget. Increase revenue (like taxes) and decrease spending (like 2, or is it 3, wars?). All the bluster from republicans to decrease spending sounds good in soundbite. However, if you look at what republicans have to cut, it isn't about saving money but about long held ideological issues. Republicans are against the reproductive rights of women, so we must cull funding to Planned Parenthood, which will save as much as $360,000,000 in 2009. Of which 3% (not well over 90% dumbass) is used for abortions. That's a shit ton! Well, not really...Planned Parenthood's entire budget was 0.011% of the 2009 budget!!! Or roughly 3 days of cruise missile attacks in Libya.

The Daily Show - Countdown to the Next Countdown - Jon Kyl's Planned Parenthood Statistics
Tags: Daily Show Full Episodes,Political Humor & Satire Blog,The Daily Show on Facebook

Unfortunately, all the bluster about spending cuts is really serving to pay for more tax cuts for the ultra-rich. If you are in debt and you take a second job to help pay the minimum payment on the new credit card you just bought a flat screen TV with, well you aren't balancing the budget, just maintaining the cluster fuck of a life you call status quo. Actually, you aren't maintaining. While taking out the new credit card to buy your new TV, you have chosen to sit on a se7en-inspired anal probe you call "balancing the budget"

Brewers Unite! at the Univ. of MN

For those interested in science and beer, the following seminar is taking place this Thursday.

3:30-5 p.m., Thursdays | 239 Gortner

"The Natural History of Beer"

Jim Cotner Ph.D.

Dept. of Ecology, Evolution & Behavior

University of Minnesota

Items of Interest

Since I wrote this recent post, I thought Ild share some related information. First, the colleague, Dr. Cotner, who is using the "penis as an evolutionary spade" paper in her class was interviewed on a local radio show (4/3/11). You can find out some information regarding her popular biology (sex) class. Also, she is giving the following seminar in the Department of Ecology and Intelligent Design Evolution Biology:

EEB Seminar
April 6, 2011
3:30 p.m.
335 Borlaug

Dr. Sehoya Cotner

A classroom full of creationists: Separating fact from fiction in evolution education

If we accept that evolution is essential—if not the key—to understanding biology, then we also have a problem: How can we understand the tendency of so many practitioners of biology to avoid teaching evolution? Recent events in the evolution-creationism controversy highlight the tensions involved in teaching and learning about evolution, and reinforce themes that have persisted for decades. My work with colleagues, from both a survey-based perspective, as well as from my experiences teaching on the front lines of introductory biology, will inform much of this discussion.  Namely, we’ll address what our students have learned prior to arriving at the University, how they perceive the evolution they are taught in class, and what, if anything, can be done to affect positive change in our students’ understanding of the discipline.

Personally, I love the accompanying picture. 

In Support of Unions: Atheist Talk this Sunday

Monica Meyer

Monica Meyer will be joining Mike Haubrich to discuss the campaign against unions in this country. Yes, they will be discussing gay marriage on Atheist Talk Sunday March 27th 9AM Central on AM 950.


Our guest this week will be Monica Meyer, executive director of OutFront Minnesota.  She will discuss their upcoming Lobby Day at the State Capitol in St. Paul on April 14, 2011.  She will also discuss the threat of the Minnesota State Legislature putting a State Constitutional Amendment on the ballot that would specifically ban same-sex marriage.


You can live stream the show, simply enter a Minnesota zip code, like 55455.

Does size matter...or shape..Yes we're talking about the penis

An older study brought to my attention recently (subscription required, though I also found this link).

This is strictly to avoid a dong
being the lead in picture on FoS

The authors want to test some ideas regarding behaviors and adaptations human males may have to ensure paternity. As I heard about this research, my skeptic meter went off and I whipped out my critical thinking tool box to look at this problem and research more closely. The colleague telling me about this research seemed to think I was being a bit of an asshole, but Im used to it.


First, we have to consider the central hypothesis that there is a fitness cost associated with human males not being sure of paternity. Obviously, raising children takes a bazillion resources so from that perspective a dad doesn't want to waste his time and energy raising Chet's kid. That explanation jives with our sense of selves in our current society, but what about 4000 years ago? Prehistorically (and historically for most of the planet) people lived as hunter-gatherers, in family units. Not being an expert in anthropology (maybe Dr. Laden will comment if he sees this post), but my understanding is that a given male in the tribe spends less time raising one specific child. Resources are acquired and distributed amongst the members, fucking socialists. So under most of human evolution, what were the selective pressures that would promote the behaviors the authors take as givens?


Even today, while there are reasons to want to ensure paternity, if paternity were a major part of male behavioral make up, presumably we would all have a dozen mistresses on the side to maximize our chances to get some paternity. Of course, while we were visiting our mistresses, our mates could use that time to help the local studmuffin with his paternity issues.


Basically, I don't like these behavioral rationales because it is trivial to argue them any way you like. We could look at the animal kingdom to gain some potential insights, but that's a clusterfuck as well. Chimpanzees, gorillas, and bonobos all have extremely different sexual behaviors. Lions kill their step children, eagles mate for life, cuckoos force surrogates, seahorse males exclusively care for the young, penguins mate for a season raise a chick then trade up or at least out. So whatever human behavior you want to rationalize, there will be an example in the animal kingdom you can use.

Modified from paper

Ok, so let's take the behavioral rationales off the table and simply look at what the authors did. One thing they wanted to test was the semen displacement hypothesis. What? You don't know what the semen displacement hypothesis is? Well, its the idea that the shape of the penis allows it to act like a scoop to remove another dudes semen if said other dude recently had sex with the woman you were currently copulating with.





The authors acquired some artificial penises (commonly known as dildos) and an artificial vagina (commonly referred to as damned if I know) and made artificial semen (cornstarch and water). The authors put the "semen" in the "vagina" and then "copulated" using the "penis". (If ever a sentence needed scare-quotes.) Then the amount of "semen" remaining was then measured to come up with the following data set.

These are the phallus types

So both dildo penis B and D, which have scoops displaced 85-90% of the cornstarch. Whereas  VibroMaxxx penis C displaced 30-40% of the cornstarch. It looks like the hypothesis is supported. However, I have some concerns. First, cornstarch isnt semen. For one thing, semen contains spermatozoa that swim, like towards an egg cell. The authors removed that variable by making the "vagina" a closed orifice. By sealing one end, there's no place for anything else to go but stay still or be pulled out. In the real world, maybe the act of secondary copulation pushes more semen and sperm of the first guy deeper into the vagina closer to the cervix and the ultimate prize the egg. That was not an option here.

Second, where have all the good sperm gone? During ejaculation, the sperm come out with a fair bit of thrust (yes, I know). While much of the semen remains within the vaginal cavity, I wonder how quickly sperm that most likely fertilize an egg leave the vagina? The vaginal cavity is not a hospitable place for sperm. It's essentially a lethal acid bath, not to mention there's mucus that you can get hung up in, and immunological cells acting like you don't belong there. Getting out of Dodge is a good thing. If we take the scooping results presented as solid, the question becomes, in real life what's being scooped out: competing healthy sperm of your best friend or the dead residuals of said ex-best friend?

Third, timing. For this hypothesis to work, it seems like a woman would have to find another mating partner in a reasonably quick period of time. How common is a rapid turn around time? If it isn't that common, there's probably little to no selective advantage because we have to factor in the chance the first guy wins anyway as well as all the times copulations fail to produce a pregnancy.

There was a lot more in the paper, some surveys (YAY!!) and what not. You should read the paper to get all the details. But color me not convinced. The idea the human penis shape plays a role in sexual competition is interesting, but there seems to be too much hand waving to justify the research. If we take these 3-5 things as givens, then.... Well, I'm not a fan of taking things as givens.

I am convinced of one thing though. If during sex, I recall that my penis may have evolved a scoop-like shape to help remove semen from a competitor, it'll probably be time to call it quits.

Interesting aside. In all of this work and study, the woman is completely neutral just a bystander in the process. If there was a penal shape competition going on, I would fully expect that there was also a role for the female in this process, she would not want a sub-par partner ruining her perfectly good plans. Women may promote successful copulations with the primary stud of interest by changing position to allow deeper penetrations during climax for one partner but not the other, for example.

Gallup, G. (2003). The human penis as a semen displacement device Evolution and Human Behavior, 24 (4), 277-289 DOI: 10.1016/S1090-5138(03)00016-3

R01s and Me

R01 grants, the standard grant that runs a lab from NIH, are now scored based on 5 criteria: Significance, Investigator(s), Innovation, Approach, Environment. Each criteria is given a score ranging from 1-10, with 1 being awesome and 10 being death. You really want 1s and 2s across the board have a strong chance at funding.

The best calendars year after year

When proposals are submitted, they go to a study section, which probably has 70-90 proposals to consider. Of these proposals, probably at best 5 will be funded. In order to give the "best" grants more consideration, grants outside a certain a range are not discussed at the study section meeting (why bother talking about #63). These "not discussed" grants are triaged. You get your scores from the study section members that directly reviewed the proposal, but no overall score. Now depending on study section, the grants actually being discussed proposals have 1s, 2s, 3s, 4s, and maybe some 5s.

A couple things to note, the Investigator and Environment scores do not vary much in study sections. Why would they? Presumably the person submitting the grant is a published scientist, generally a faculty member at a university or research center and the environment is where the research is done, university or research center. The one score that seems to matter most and tracks with the "Overall" score is Approach.

I have been submitting a bunch of proposals recently, who hasn't, and thought I'ld share some of my experiences. Now every study section is different and scores/trends in scores can vary markedly, so my experience may not apply to you. I should note that of these proposals, 3 were submitted to the same study section an the other 2 were submitted to different study sections (1 has funded me in the past), but all study sections were within the same Institute of NIH.

Remember the scores are for Significance, Investigator(s), Innovation, Approach, Environment. I have used the code S I I A E to represent  these respectively. So here are the scores for 5 proposals I have submitted recently and you should note that all of these proposals were "Not Discussed" (Yes, it does suck to be me sometimes.)

Grant 1         S  I  I  A  E
Critique 1     3  3  3  4  3
Critique 2     3  2  2  4  2
Critique 3     6  3  6  6  2
(Comment: Fucking reviewer #3)

Grant 2         S  I  I  A  E  (Similar types of analyses as Grants 1 and 5)
Critique 1     7  5  6  8  2
Critique 2     5  2  7  3  1
Critique 3     4  4  6  5  4

(Comment: Environment 4?!?! Apparently Reviewer #3 thinks my major research institution is not all that cut out to do the basic molecular genetics work I have been doing for a decade)

Grant 3        S  I  I  A  E  (Change in research focus, completely different study section)
Critique 1    3  7  8  8  6
Critique 2    6  4  8  7  3
Critique 3    7  4  6  7  4

(Comment: Alright this proposal either sucks or was sent to the completely wrong study section. Actually both possibilities could be true. Check out those Approach scores 8, 7, 7. Charlie Sheen would tell me Im Winning. Regardless, mistakes were made. The amount of time needed to put together an strong R01 proposal in my opinion takes too long to use )

Grant 4        S  I  I  A  E  (Similar types of analyses as Grants 1 and 5)
Critique 1    4  2  3  6  2
Critique 2    3  2  3  4  1
Critique 3    5  2  3  3  2

Grant 5        S  I  I  A  E  (A1 of grant #1 above)
Critique 1    3  2  3  3  1
Critique 2    3  2  3  3  2
Critique 3    5  2  4  4  1

(Comment: Fucking reviewer #3...again. This really sucks because this grant is now considered dead. An A1 proposal, a resubmission, cannot be put back in without major fundamental changes. So here is a grant that is reasonably close to the funding area, but it cannot be honed it must be fundamentally altered. Is this really the best use of my time NIH?)

So Grants #1 and #5 (5 was a resubmission of 1) are close and by my reading missing some Omph in the sales department. I will figure out a way to keep at it with this project (Im looking at you NSF). Grant #4 has another shot, although that 6 and 4 under Approach mean serious work has to be done to beef this one up. Grant #2 needs to go to the study section #1, #4, and #5 went to, looking back I directed it incorrectly. Grant #3 requires another publication, a complete rewrite/focus, and a new study section. I think Grant #3 is dead and will ultimately evolve into Grant #6, 7, 8, or whatever number Im up to by then.