Field of Science

Minnesota State Academic Science Standards

I am happy to inform you of your selection for the Minnesota K-12 Academic Standards in Science Revision Committee. We received 115 applications and are pleased that so many parents, educators, business and community representatives are interested in helping us revise the science standards to reflect the high expectations that Minnesotans hold for our children and youth. I sincerely appreciate your dedication of time and effort to this important project.
During the first meeting, we will present an overview of the standards revision process and will identify criteria for high-quality content standards. A large block of time will be reserved for you to review the feedback submitted by the public via our online survey. The feedback consists of suggested improvements to the current science standards. You will have the opportunity to read and discuss suggestions submitted for each standard or benchmark and provide direction for needed changes.

Well, well, well, yours truly was chosen to help in this important process. I am looking forward to these meetings, which should be a learning experience for me. A couple of points I am thinking about right now. First, I probably will not blog about any of these, or subsequent, meetings. I would not want committee members feeling restricted in expressing their thoughts if they thought these thoughts may end up being viewed by my vast audience of ~2. /waves to wife and kid

Second, I couldn't help but wonder if my name had anything to do with being chosen. My wonderment was based on the following: "Dear Ms...." The joys of having a unisex name, at least mine is rare enough that it wasn't a problem during those traumatic elementary school years. However, the committee is well balanced by gender and may in fact favor female members to male members by 1, if my quick count was accurate. For those interested in the process, standards, committee reps, etc check out the MN Department of Education science standards and follow the links at the bottom of the page.

A Tangled Bank

A new, and my first, tangled bank is out over at Greg Laden's Blog. Grab a cup of joe and check it out.

Happy Birthday to me!

Yes, it's my birthday today, another successful trip around the sun. What to do on this special day, work on two papers the need to be resubmitted and submitted, finish up an overdue review, and check out a school for my boy. Oh, and most definitely not eat salmon mousse!

My Current Political Testing

You are a

Social Liberal
(76% permissive)

and an...

Economic Liberal
(21% permissive)

You are best described as a:

Socialist (21e/76s)

Link: The Politics Test on Ok Cupid
Also: The OkCupid Dating Persona Test

Monday Journal Club...

will return next week. Last week I had to miss out and this week I presented a paper I already discussed for those who might need a fix.

Creationist "Science" Fair

Well despite some advice and my better judgment I went back to the homeschooled children science fair put on by the Twin Cities Creation Science Association (TCCSA). Already you know that this is a sub-group of the population of homeschooled children (although we would have to be fairly naive or downright stupid to think this is not the majority viewpoint). I was there before the parental mouthpieces, aka children, arrived, so I was unable to ask them any questions. Regardless, I am left with a mixed opinion, I am torn between anger and sadness.

First anger. One very nice poster, which I was glad to see won a first place ribbon, was on ways to keep cut flowers from wilting. This student took flowers, one kind, and put them in water with a variety of compounds, including the powder that comes from floral shops and aspirin, which even I have heard helps keep flowers last longer. Her hypothesis was that the stuff from the florist shop would work best, but found it didnt't work better than water alone (similar results for aspirin as well). Some of her other tests, like a dilute bleach solution and, I believe, baking powder actually kept the flowers fresher longer. While this is nice, what separated it from every other poster there was her analysis of the data. First, she noted where she screwed up the experiment and how it might confound her results. She suggested the experiment should be repeated and outlined the way in which she would alter the design to make more reproducible. Her analysis was really a beautiful example of real science is done. Of course there was a throw away bible verse on the poster, which mentioned god and flowers, but had no bearing whatsoever on the hypothesis, experimental design, or interpretation. I do not begrudge this student using it, since the guidelines strongly encouraged the students to put a verse on the poster, and I expect a poster without the obsequeious verse would not be receiving a blue ribbon. So why am I angry? Well, this student could have participated in any science fair and done well I expect. But since she was at the Creationist Science™ fair, I expect her scientific thinking skills are going to be malnourished and not fertilized. Here is a student, who could potentially flourish in medicine, veterinary science, public health, engineering, etc. Maybe she would make the key insight that leads to a way to reduce the risk of autism or prevent alzheimer's disease. However, I expect her parents are more likely training her to be a baby-maker who defers all decisions to her holyroller GED equivalent future husband. I could be, and hope to be, wrong, but this was a creation science fair for homeschooled children, not a homeschool science fair.

Now the sadness.
1. Another blue ribbon. This was a report on duck egg incubation. Well it was a poster, but really it was a report. There was no experiment or data, just some facts like eggs have to be rotated to keep all areas warm. Clearly, there are going to be differences between different grade levels and this may be an example of that. However, my 5 year old has already looked to see how much bacteria is on his hands before and after washing in a qualitative way. So, no hypothesis, no experiments, what could be the conclusion? Ill just quote from the poster, "I think its amazing how ducks grow in their eggs and I know god created them." Lovely.

2. A second place winner. This was a report on motors and irreducible complexity. Yes, the student took a simple motor apart and guess what? It didn't work as a motor anymore. I wanted to ask him, if the pieces would work as a paperweight, but that probably wouldn't have gone over well. Someone should take away the parents' homeschooling accreditation.

3. We had a test of the hypothesis that the biblical flood could create geological features like the grand canyon. This was a beautiful study in that the "student" took wet sand as a substrate and poured water on it and lo like moses at the red sea, the earth parted. Well it was moved by the water making a nice little channel. Clearly, if a little water can make a channel then the global flood could make the grand canyon in 150 days. I wanted to point out the sides of the grand canyon, at least when I was there, are made out of hard rock not wet sand. I also wanted to ask him, if a little water was so powerful, how are we able to drive across bridges over the Mississippi or any other river. Shouldn't we need to rebuild the bridges about every 6-10 minutes based on the conclusions of this cutting edge research. Note, I am not teasing the student here, I am railing against the ludicrous parents and their idea of education.

4. Another project, which had merit, was based on the conjecture that some guy showed that habits form in people after 21 days. This student wanted to know if dogs obtain habits faster, the hypothesis being that animals will learn habits faster than people based on some bible verse. Being as the bible is inerrant, the conclusion is a forgone conclusion. The student trained the dog to run through her legs and it took less than 11 days to complete the training. Thus, the dog learned a trick (for which there must have been a reward) faster than a person picks up a habit. The student is on the right track here, seems to be thinking about things. However, a cursory analysis of the experimental set up would reveal the fundamental flaws in the logic. Another thing worth noting to me, is that this hypothesis is based on the word of someone. There may be hard science to support the 21 day conjecture, but I didnt see a reference on the poster, only statements like XXX showed it takes humans 21 days to develop a habit. While I am reading much into this, I find this is a good example of an appeal to authority, which is bread and butter with christian thought. Some pastor says something, thus it is true.

5. Lastly there was another 2nd place finisher looking at food and body pH. This one struck me because I think about pH a lot and this is an area of alternative medicine getting more popular. Basically, if you eat or drink something acidic or alkaline the pH of your mouth will change. This is extremely well documented. I infer the student measured their salivary pH using pH paper some time after eating some type of food with a given pH. This was done once a day (unclear if this was controlled for time of day) and I could not figure out how much of the food was consumed. If you eat some alkaline food, followed by a can of pepsi, you have screwed your experiment. Also, it is unclear how the food you eat would change your body's pH, remember these foods pass through an organ the secretes a fair amount of hydrochloric acid.

Not everyone can be a productive scientist. The population who can really do something special, and I do not include myself in that class, is already small. Here are 6 children who will have very little chance to be one of these people.

Homeschool science fair at HarMar

Yes this is the weekend that the abortion travesty called the 2008 Home School Science Fair is held at Har Mar Mall in Roseville Minnesota. I stopped by briefly, until my protege had a meltdown got a time-out and we had to leave. I might load up on Maalox and try to make it down tomorrow. Anyway what I saw was depressing. The Science™ presented was...Im actually at a loss to describe it. In part, I feel for the kids who are being told they are actually doing science and are using the scientific method. I shouldn't be surprised, I mean this is put on by the Twin Cities Creation Science Association (TCCSA). Their website is clearly a monument to the scientific process, I refuse to link to it but you can find it easily enough.

The indoctrination these children are getting is horrifying. They are encouraged to include the bible verse related to their hypothesis on their poster. See its all about the science, not a preconceived viewpoint. Sadly, I see an intelligent student being set back, probably forever, thinking that they are actually participating in the scientific process when really all they are doing is advertising. "My experiment, to see which battery can generate the most light (based on some bullshit verse with the words god and light in it) worked, eureka I have evidence that the bible was right." These students will then grow up thinking there are two types of science, fundamentalist christian science and satan science. They will then vote for the husband of a Bush daughter (because women will not be eligible to be president in the future. They will be wearing clothing completely covering the face and body, which will not be burkas, because burkas are from that evil Islam culture, nope these will be called christkas).

And some people wonder why Dawkins posits religion as a form of child abuse.

Intelligent Design=Fuck science Go PR!

You know, I hate the promoters of the "intelligent design" movement. They are liars, blatant, despicable, loathsome liars. These maggots sell false information, which they know is false, in order to get a political (theological) viewpoint pushed forward. They are too chickenshit to stand up for what they believe in. Rather, they work in the shadows, slinking around like the evil foul bloodsucking bastards they are. Case in point the movie "Expelled." Here's an email making the rounds (names were changed to more actually reflect the sender's brain power).

Expelled Movie Starring Ben Stein
Posted by: "Ima Dumass"
Tue Feb 12, 2008 12:16 pm (PST)

Please pass this VERY important information along to
anyone you know who may
be interested. Thanks!
Ima Dumass

Use of an all caps VERY does indeed make this email more relevant.

EXPELLED teams up with the Discovery Institute to
launch the Academic
Freedom Petition, EXPELLED receives endorsements from
James Dobson and more!

So the Discovery Institute promotes Academic Freedom! I thought they promoted the following:
Twenty Year Goals
* To see intelligent design theory as the dominant perspective in science.
* To see design theory application in specific fields, including molecular biology, biochemistry, paleontology, physics and cosmology in the natural sciences, psychology, ethics, politics, theology and philosophy in the humanities; to see its innuence in the fine arts.
* To see design theory permeate our religious, cultural, moral and political life.
This is from the Wedge document, clearly they have a strategy to make their viewpoint the dominant viewpoint. Interestingly, it does not matter what the evidence is, they have a goal and will fit/ignore/fabricate any data accordingly. Viva l'academic freedom.

HOLLYWOOD, Calif. (Feb. 11, 2008) - With nothing less
than truth and freedom
at stake, the producers of EXPELLED: No Intelligence
Allowed and Motive
Entertainment have teamed up with the Discovery
Institute to launch the
Academic Freedom Petition. The petition urges
America's academic
institutions to adopt policies to ensure teachers and
students have the
freedom to discuss the scientific strengths and
weaknesses of Darwinian

They should already be shouting success. We already discuss the strength of evolution and discuss the areas of discrepancy, consider the idea of punctuated equilibrium. What these people mean, in no uncertain terms, is they want the consideration of fundamentalist creationism (rename it intelligent design, its the same poison). What the Academic Freedom Petition is for is for protection of religious nutjobs who sell creationism or other christian perspectives (flat-earth, young earth, π = 3) as science or math etc.

On another front, EXPELLED star comedian and Nixon speech-writer Ben Stein and the
producers have been
traveling the nation to meet with key leaders and
screen the movie.

Of course this has been done in an honest and upfront fashion, you know because these are good christians promoting a more moral and righteous worldview.

has received strong support already!

I wonder why?


"Ben Stein's film, EXPELLED, makes a powerful case for
Intelligent Design in
explaining the origins of life and the creation of the
universe. It also
exposes an entrenched and aggressive Darwinist
establishment in academia
that suffocates all competing points of view. Highly
qualified professors
and scientists who dare to question evolutionary
orthodoxy are
systematically excluded or summarily dismissed. It is
political correctness
run amuck on university campuses. Stein sets out on a
mission to find out
why I.D. Is most often expelled from the public
square, and what he
discovers in this riveting documentary is incredibly
enlightening. I
recommend the film enthusiastically. "
- James C. Dobson, Ph.D., Chairman of the Board, Focus
on the Family

Ah yes, the powerful case. Let's see, scientists have all the data. So I guess the powerful case for intelligent design is that someone who knows very, I mean VERY, little biology can easily understand intelligent design and it fits in neatly with their preconceived world views.

"This is an enormously important project and I am so
proud of the fact that
Ben Stein, who is a national treasure
let's bury him then, is part of it.
People know that there
is a dictatorial impulse at work in the land to shut
down even the most
elementary questioning of this unquestionable belief
in random evolution and
the American people don't like being told by their
'betters' what they are
supposed to believe."
- Michael Medved, nationally syndicated radio host

Its true any old ignoramus should be able to have whatever facts™ they like and have those facts™ be equal to the facts found through painstaking research and effort. God™ forbid someone, who has studied for years and thought deeply about an area (aka 'betters'), might actually know more about said area than your local dittohead. Here's a thought Medved, next time you need a doctor, have the local Kmart checkout person fix you up, I mean you wouldn't want one of these 'betters' acting like they know something.

"EXPELLED: No Intelligence Allowed is earthshaking. I
was absolutely blown
away. Ben Stein boldly shines a light of honest
inquiry revealing that
evolution's emperor has no clothes. It will have
Darwin's disciples
scurrying for the shadows. Everyone in America, even
skeptics of Intelligent
Design, must see this film. They can't possibly walk
away without at least
admitting that the debate over who we are and how we
got here is far from
over. The controversy will be intense, so get ready
for a rollercoaster ride
- J. Matt Barber, Director for Cultural Issues,
Concerned Women for America

True, everyone may walk away from a movie admitting there is a debate. I mean, since you have no evidence, or predictive value to your "theory," make a movie. Its not about science, its about public opinion polls.

"EXPELLED: No Intelligence Allowed offers a compelling
examination of an
important topic for everyone who values the freedom to
explore ideas that
challenge conventional wisdom. Ben Stein has given us
a powerful documentary
about the widespread repression of faith-friendly
scientific scholarship.
Along the way, he also makes a strong case for a
return to civil discourse
in a time when political correctness often overshadows
the search for truth.
EXPELLED is an engaging film that features a winning
combination of humor
and reason with just the right tone needed to bring
its significant story to
the worldwide audience."
- Ronald D. Ellis, Ph.D., President, California
Baptist University
Read more at: www.GetExpelled. com/quotes. php

Civil discourse?!?! Hey Ben Stein, Fuck off! The last thing these people are interested in truth. They insult the very word by using it. These people routinely lie, they quote people out of context to change the meaning of their words, they make up facts to suit their purposes. They are not interested in the truth, they are interested in ensuring their tiny little worldview is mandated to the rest of the country. The fact is, they have dedicated themselves and defined themselves around one very specific interpretation of the bible. Any evidence that disagrees with this viewpoint must be squashed. While they don't speak for all christians, they have too much political power to be overlooked. There is one positive, not that long ago when people presented viewpoints that contradicted the viewpoints of these types of christians, these people were stoned to death or burned to death. Now we go on a PR campaign to malign and otherwise try to push to the fringe those who have alternate viewpoints (particularly when those viewpoints are supported by mountains of evidence.

We need your support! Here's what you can do to help
spread the word about
the movie EXPELLED and stand up for academic freedom:

Note they don't ask you to do any research or think about the science.

Send an email to all of your contacts informing them
to learn more abou t
the film by visiting www.GetExpelled. com and
encourage others to spread the

Go to your local theater and speak with a manager to
request that EXPELLED
is shown in your city. The movie is coming out this
April and you can print
off a movie poster for the theater's reference by
visiting www.GetExpelled

Buy advance tickets for your family and friends to see
the movie. Invite
everyone to see the film during opening weekend in
April 2008.

Add a banner or post a video clip to your website,
MySpace page, Shoutlife
page or blog. You can access our Tools for Webmasters
by visiting www
GetExpelled. com. We have various free resources
available for your use.
Help spread the word in your local area churches,
schools, clubs and
community centers. For more info, please email:

Here it comes...

Stand up for academic freedom and freedom of
scientific inquiry by signing
the petition at: www.academicfreedom petition. com.

This is not about academic freedom or inquiry (or even free speech). This is about special protections for an idea that has been
absolutely destroyed from a variety or perspectives. But yet we waste time and energy dealing with it.

The EXPELLED resource website - www.GetEXPELLED. com -
has added some
exciting new features. The site is packed full of
useful tools and resources
to promote the ideas surrounding this history-changing
film, which opens in
theaters this April:

Learn about new scientific evidence that invalidates
Darwin's claims.

Well, there is no new old or other evidence that invalidates evolutionary theory. Yes, specific claims of Darwin are obsolete. Of course science, unlike religion, changes over time as new information comes to light. Creationism/intelligent design are the same interpretation of the book of genesis.

Hear from scientists who are being SILENCED for those

Not for failing to publish papers or obtain significant grant support. Of course not, its all a big conspiracy. Woooooo (scary sound ghost)

Learn how to DEFEND BELIEF in God based on SCIENTIFIC

And there it is. This is all about forcing a specific christian belief on the rest of us. This is not about science. Of course, if by god they mean Vishnu, I might have to rethink my concerns. Regardless, evolution only disproves a christian god, if you are so closed minded as to buy into a literal interpretation of genesis. This is the same bullshit used to conclude the earth is flat and that the sun revolves around the earth. Scientific thought changes as new information comes to light, religion it stays the same. The problem most atheists have with religion is that religion constantly oversteps its boundaries. I know of no established religion that explains how the universe works that fits the evidence. So, either the evidence is wrong (and much of the things we generally depend on like cell phones and medicine is really done by invisible elves) or the religion is wrong. There are many christians who adapt their worldview to fit the evidence, one good example is Ken Miller. These are the kinds of people I like to hang out with.

Learn what can and cannot be taught in schools and how
that is CHANGING

Homeschools dont count. Regardless, if these assholes get their way, they will legislate what is scientific theory. If you don't have evidence or data, get politicians to force it into schools.

See a SNEAK PEEK of exclusive video clips from the
upcoming movie.


In this film, author, former presidential
speechwriter, economist, lawyer
and actor Ben Stein exposes the frightening "atheist
agenda." The film also
reveals how teachers, students and scientists are
being "expelled" and
persecuted for questioning Darwinism despite the
mounting evidence that
debunks Darwinism and shows proof of a Designer
("God") in the universe!
This highly controversial documentary is receiving
major media buzz
(including the front page of the New York Times). In
the movie, Stein
travels the world, asking top scientific minds whether
Darwinism is still a
theory" or if it's become a "law" which no one is
allowed to question.


The second leg of the EXPELLED Nationwide Tour wrapped
up in late January.
The EXPELLED team traveled from Texas to Miami before
heading north to the
nation's capitol. The guys in the big, red EXPELLED
bus met some amazing
people along the way, including EXPELLED star Ben
Stein himself. Ben
attended a screening in Orlando for about 3,000 Young
Life leaders. He was
incredibly gracious and stayed to sign autographs for
everyone in line.
Following a screening at the Heritage Foundation in
Washington, the EXPELLED
crew passed out information on the film at the March
for Life, which drew
over 30,000 people. The tour continues with stops in
Georgia before heading
back to Florida and Texas. Tour details at:
www.GetEXPELLED. com/tourblog

SHOUT OUT and let your voice be heard! Tell us about
your own Expelled
experience and possibly win the chance to be in the
movie! Click here for
more info.


Paul G. Humber, Director
Back to top

I am not intolerant of christians per say, but I sure would appreciate it if those of you more rational christians would speak out against these people. The discovery institute, Ben Stein, Pat Robertson etc. these are your representatives. If you don't like it, get more vocal.

The Joys of Science

This is why soft skinned people should not be in science. In the last week I have had 2 papers rejected from top-tiered journals and of the 4 abstracts submitted from my laboratory to a national meeting, exactly 0 were chosen for oral presentations. Too bad I don't have a grant under review right now, I could go for the trifecta.

Monday Journal Club: February 4th edition

Today's journal club was a discussion of the paper Self-Regulation of Candida albicans Population Size during GI Colonization." by White SJ, Rosenbach A, Lephart P, Nguyen D, Benjamin A, Tzipori S, Whiteway M, Mecsas J, and Kumamoto CA. in PLoS Pathogens 2007 Dec 7;3(12):e184.

For full disclosure I chose and presented this paper. I picked this paper for several reasons. First, I am a strong supporter of open access journals, such as PLoS pathogens so I wanted to advertise. Second, the area is of interest to me and hits on an important topic. Third, there are a couple of potential teaching points, one of which hits on a point we covered last week.

Candida albicans is a commensal (this effectively means the organism does not harm or benefit the host, although this is a point I'll try to touch on in another post) in essentially everyone. C. albicans lives throughout your digestive system including your mouth, esophagus, and intestinal tract and in the vaginal tract. C. albicans is generally well known as the causative agent of thrush (oral candidiasis) and vaginal yeast infections. It is also the primary cause of diaper rash (so antibiotic diapers generally are useless because they kill bacteria not fungi, but they market well to young mothers). However, unlike many organisms, you don't find C. albicans in the environment, in other words, C. albicans' natural niche is the human mucosa. C. albicans does infect other mammals particular in a zoo environment, however it does not appear to naturally colonize these other mammals. While mucosal infections, like thrush and vaginitis, are problematic, they are generally not life threatening. However, if C. albicans enters the bloodstream, it can disseminate to virtually every organ, including kidneys, liver, bones, heart, and brain, and kill you. This disseminated infection is called systemic candidiasis. Now these systemic infections require a host with an impaired immune system, including organ transplant patients and chemotherapy patients. Because C. albicans can cause infections if conditions are favorable, it is considered an opportunistic pathogen. What's interesting, is that the C. albicans that cause these systemic infections are the C. albicans organisms that normally reside in you gut. It is the C. albicans you are already carrying that causes these life-threatening infections. This is different from many other organisms, like E. coli, where the flora within you is generally not disease causing but variants from the environment are. Ok, long introduction to get to the main problem being addressed in this paper. We know very little about how C. albicans colonizes and grows as a commensal or how it escapes from the GI tract to the bloodstream as an opportunistic pathogen.

This paper uses a piglet model and mouse model to look at gene expression changes in C. albicans when it is in the GI tract compared to a control laboratory environment. They identify several genes including EFH1 which was expressed more in the GI tract, compared to the oral cavity or laboratory conditions. They then go on to study EFH1 in a little more detail. However, I want to point out a couple of problems I had with the aspect of the paper. First, the number of samples used was very low and only from the pig model. In fact, they only used 2 oral samples and 1 intestinal sample! An n of 1 does not a strong position make. That's not to say the results are incorrect just tenuous at best. It would have made me happier if they had also looked in the mouse GI samples to corroborate the pig data. Second, they compare the C. albicans from the pig model with laboratory grown cells. This is always going to present problems because the conditions are fundamentally different. Here, the onus is on the researchers to make things as close as possible, and I thought they fell short of the mark. For instance, the authors grew C. albicans in the laboratory at 34°C whereas the body temperature of the pig is ~39°C and the mouse is ~37°C, so there is a 3-5 degree difference (yes, this can be significant). What bothers me here is that you can grow the cells in the laboratory at whatever temperature you want trivially. So Im left wondering, what the hell? Next, they grew the cells in he laboratory in a yeast extract, bacto-peptone, sucrose solution. Not what I expect the gut of a pig or mouse has. Some alternatives could be an extract from the grain/oats/or whatever the animals are fed or an infusion from an animal source, such as beef heart (commonly used) or even pig intestine! Finally, they use logarithmically grown cells in the lab, whereas the C. albicans in the animals are almost certainly primarily in stationary phase. In fact, the authors go on to show that all but one of the genes they identified are expressed preferentially in stationary phase cells compared to logarithmically grown cells. In short, the part of the paper identified C. albicans genes expressed in the animal because C. albicans in the animal are not rapidly dividing.

The authors go on to characterize a gene called EFH1, which encodes a transcription factor of unknown function. They take a genetic approach and delete the gene and then look to see the effect. Surprisingly, they find that the efh1∆/∆ mutant colonizes the mouse intestinal tract better than the wild-type EFH1/EFH1 strain. This is surprising because we generally think more is better. Thus, we expect that wild-type C. albicans grows the best in the host and the only phenotype we would see is less growth in the host, not more. I mean how could a mutation make the cells grow better!?!?! There's lots of reasons, such as loss of this gene makes the cells grow better in this specific system (which is not relevant to the natural system), but in other important ways not addressed in this model the mutant is dead on arrival. So the positive selection observed in this model would be balanced by the strong negative selection under other conditions.

Ok, we have an interesting unexpected phenotype, what to do now? From my last journal club , you probably know the answer is a complementation test. Yes, put a wild-type copy of the EFH1 gene into the efh1∆/∆ mutant and look to see if the phenotype is restored. Well the authors did this and found that the efh1∆/∆ +EFH1 strain actuall grew worse than the wild-type strain. In other words, based on growth in the intestine of a mouse efh1∆/∆ > EFH1/EFH1 > efh1∆/∆ +EFH1. In the perfect world, you would expect efh1∆/∆ > EFH1/EFH1 = efh1∆/∆ +EFH1. So why the discrepancy? Well for one the researchers used a strong promoter to express the complementing EFH1. So the amount of EFH1 mRNA, and thus Efh1 protein, will be different. This could be the issue and is the one favored by the authors. It provides evidence that suggests the amount of Efh1 protein controls how much C. albicans growth occurs in the intestine. This is really cool!

With a really cool result comes a higher bar than would be seen with an expected result. So do the authors reach a higher bar? In my opinion no. For starters they never showed that the amount of Efh1 protein (or mRNA for that matter) is actually any different under these conditions. This seems like a fairly obvious requirement. Also, the genetics were not as rigorous as I would expect. First, they introduced their complementation construct into the endogenous locus and it didn't work. They note that others have seen this problem, which means its ok. Nice sloppy reasoning there, "others couldnt figure it out, so why should we." They also use express EFH1 from the promoter of another gene. This is often done, but its usually for a scientific reason. The authors provide no justification for this, which is odd. Finally, the strains they compare are not appropriate.
Their mutant strain has the following genotype:
arg4∆/∆ his1∆/∆ ura3∆/∆ efh1::ARG4/efh1::HIS1 leu2::URA3/LEU2. This strain is deleted for ARG4, HIS1, and URA3, two markers ARG4 and HIS1 are used to disrupt EFH1 and URA3 is introduced into the LEU2 locus to make the strain prototrophic again. Since C. albicans is diploid this strain has 1 copy of ARG4, HIS, URA3, and LEU2; 0 copies of EFH1.

Their overexpression strain has the following genotype:
arg4∆/∆ his1∆/∆ ura3∆/∆ efh1::ARG4/efh1::HIS1 adh1::P-EFH1::URA3/ADH1.
This strain is deleted for ARG4, HIS1, and URA3, two markers ARG4 and HIS1 are used to disrupt EFH1 and URA3 is introduced into the ADH1 locus along with the complementing EFH1 allele. Since C. albicans is diploid this strain has 1 copy of ARG4, HIS, URA3, ADH1, and EFH1; 2 copies of LEU2. Also, note that URA3 is expressed from different sites in the genome.

So the mutant and complemented strain they are comparing differ in EFH1 (important, this is what you are testing); LEU2 and ADH1 copy numbers and site of URA3 integration (inportant, these can confound your results since they are genetic differences). So we have the authors hypothesis Efh1 protein levels control C. albicans growth levels in the intestine. But we can consider other hypotheses, how about loss of one copy of ADH1 reduces C. albicans growth in the intestine and there is no complementation whatsoever. If we inhibit cell wall synthesis in the efh1∆/∆ mutant, growth will be reduced but that doesn't mean Efh1 protein promotes cell wall synthesis. Based on the way the experiment was done, I do not find a strong evidence that the authors actually did get any complementation. This gets back to an earlier premise I made in the first journal club, when you get unexpected or novel results, the bar is higher to ensure you are likely correct. This paper establishes some new approaches to study C. abicans intestinal colonization, but fails to reach the level of rigor to establish the surprising result that Efh1 protein controls the levels of growth of C. albicans in the intestine.

Congress does its job

In a wake of numerous scandals, having had the rule of law discarded and ignored, and overt falsifying data and lying to the general public, the Congress of the United States is taking action! How long has the Congress sat by like a bunch of emasculated old men letting Bush-Cheney run roughshod over the Constitution and our basic civil liberities. Yes, that's right the Senate Judiciary is asking questions about destroyed video tapes from the CIA torture of prisoners New England Patriots on other football teams. Yes indeed the priorities of the country are intact and maintaining a sense of complete fuckedness. Ild like to write something about science or some other topic I think is important, but I really need to go find out if Britney stuck a pencil up her nose or did any other asinine things, since that's what we really care about.

Ill post more when Ive decided I give a shit again.