Brainbow mouse!

Someone made a comment about "Brainbow" mouse, the 18th place winner in this year's Nikon Small World Contest. If you want to see all of the top twenty winners just click here.

Here's my favorite ... "Brainbow" transgenic mouse hippocampus:

Glowing Green with Envy

In all of this election clamor, I forgot to post the winners of the Nobel Prize in Chemistry for this year. The award was split between three scientists for their discovery and development of Green Fluorescent Protein or GFP: Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien.

I think this prize was rightly awarded this year. Their discovery boosted a huge jump in basic science research by pioneering a new tool that could be used to investigate questions about that molecular world. GFP was originally discovered in the jellyfish, Aequorea victoria, and is known to give that iridescent glow to our sea-water friends. This natural sort-of night light is not uncommon in the animal kingdom. It turns out that bioluminescence has evolved independetly about 30 differents times in organisms we see today. Another example is the firefly which uses a protein called luciferase to activate a substrate which will the glow after cleavage. GFP is different, however, because it can fluoresce on its own, with no need for a substrate.

The implications for the discovery of GFP have been far-reaching, and I'll just touch on a few in the biomedical sciences. GFP is a protein coded for by a gene in the jellyfish. Scientists were able to cut this gene out, and put it in other species to make them glow - first, by just making it glow in all the cells for a proof of principle. Then they began to put different promoters in front of the gene, or 'switches' that can control whether or not the gene is on or off. For example, if Gene X is only turned on in the stomach and I want to put GFP only in the stomach, I'll take the 'switch' for Gene X (usually sits right in front of the gene) and put a copy in front of GFP so that it only turns on in the stomach. This way, scientists could label particular organs, tissues, or even single cells to carry out different studies.

But what about more than one cell type? No problem - scientists have tinkered with GFP to make RFP (red), YFP (yellow), BFP (blue), CFP (Cyan), mStrawberry, Tomato, Cherry, Plum, Katushka, Kate, and the names just get better and better. We can label all sorts of cells differently and all at the same time!

What's even cooler, is that we can actually engineer a normal protein that has a normal function in a cell to have GFP at the end of it, literally attached to it. This way we can follow around single molecules inside a cell to see where they go and what other molecules they interact with!

Other strategies have used this type of labeling to sort out cell types from complex tissues using a machine that recognizes the fluorescent color.

These examples just scratch the surface of the kinds of techniques GFP has allowed us to explore. I'll leave you with a picture I took of one of my embryonic mouse gonads using a transgenic mouse line using GFP. This is a picture of an E12.5 mouse testis from an Oct4:EGFP embryo - that means only germ cells are labelled - in this case, I've psuedocolored the GFP positive germ cells to look PINK, so don't be fooled - I've labelled two other molecules: laminin and PECAM.

Behold the power of GFP:

Cellular Manipulations ... Stem Cells on the Rise

Just last week in the peer-reviewed journal Science, a report was published detailing how to generate induced pluripotent stem cells (or iPS cells) through genetic manipulation without the use of viral vectors. This work was submitted by Keisuke Okita, Masato Nakagawa, Hong Hyenjong, and Shinya Yamanaka.

Dr. Yamanka and colleagues previously published research detailing their work creating iPS cells using retroviral and lentiviral vectors that randomly incorporate into the genome of the host cell. These incorporated genetic components used only three genes: Oct4, Sox2, and Klf4. The resulting iPS cells could differentiation into any cell type.

Though promising, clinical progress would be limited due to safety concerns using retroviral/lentiviral infection - it turns out this poses a seroius risk of activating or inactivating important host genes that could ultimately lead to cancer or other disastrous consequences.

Using this new plamist transfection reported this month, that risk is averted - though the efficiency of manipulation is actually lower. The successful cells could still be differentiated into progeny of all three germ layers, indicating the continued power in iPS cells derived using this newer method.

While efficiency issues still need to be worked out, this is a huge step forward and could soon be translated into the clinic with a lot more hard work.

Evolution is ... Jewish?

One of my friends sent me a link this week to a website that exposes a particularly sinister PAC called the 'Fair Education Foundation.' Upon initial examination you might suspect that this is some sort of joke, but after careful scrutiny you'll find that the people behind it are quite serious.

It turns out that this particular exposure is a little dated (from Feb of 2007) but worth an entry on my blog for the sake of demonstrating the kind of kooks you can find trying to tamper with our government.

The following is a memo purportedly sent from the office of Ben Bridges (R-Cleveland, GA) and concerns how to combat the teaching of evolution in the public school science classroom:
Particularly interesting is the strategy: since creationism and intelligent design (ID) can't be taught in the science classroom because of their religious agenda, Mr. Bridges will attempt to make evolution the agenda of Judaism. I'm sure they would love to live in this fantasy world where they can defeat evolution/science while also scoring points against another rival religion. Too bad this is one of the most absurd ideas and would never fly in a court of law.

Overlooking the apparent anti-semitism, the supporting evidence that is offered is the best part of the whole ordeal. The actual website for the PAC also includes further information about our planet and universe. Specifically they suggest 'evidence' for the idea that our planet does not revolve around the sun, but that it is suspended motionlessly in space by magnets ... magnets that were placed by god, no less:

So the take home message is that according to the Fair Education Foundation not only is evolution a lie from a cult Jewish sect, but the heliocentric model of our solar system is blatantly incorrect - all evidenced by scriptures from the christian bible.

It's sad that they believe this - though it's even more depressing that while Ben Bridges denies issuing this memo, claims to support it more than he would 'evolutionism' or 'big bangism.' To be exact he says, "I agree with it more than I would the Big Bang Theory or the Darwin Theory,” ... “I am convinced that rather than risk teaching a lie why teach anything?"

He is a state REPRESENTATIVE! Well, why would we expect someone who graduated from Barber College to actually understand basic 7th grade science?

Ontological, Schmontological!

Well, the final presidential debate is over, and not a moment too soon. I'm so tired of stump speeches, negative campaigning, and cliché pandering I could almost go vote for Ron Paul ... almost. If all else fails, we can just get Joe the Plumber to run our country.

At the very least it would be nice to listen to a real debate. If I wanted to hear weak arguments employing poor logic that is essentially lost in semantics or word play, I'd go listen to a religious believer or deist try to convince me of god's existence using a classic ontological argument.

So, why is the ontological argument so silly? For starters, it's essentially a tautology - an argument that takes as a premise its own conclusion. Let's examine one of the more classic interpretations:

1) By definition, God is perfect and thus greater than anything a human being could imagine.
2) If you can imagine something, it would be 'better' or 'more perfect' if that imaginary thing were actually real.
3) Therefore God must exist.

Confused yet? It's saying that if you try and imagine a 'God', he's probably perfect (meaning lots of fun things like awesome, good, the best). The twist (and assumption) is that if you can imagine something incredibly crazy cool, wouldn't it be that much COOLER if what you imagine actually came true?! If 'God' is perfect, and a perfect real thing is better than a perfect imaginary thing, then by the definition that perfect is more perfect in reality 'God' must be real.

This is as much word play as it is anything else. The base assumption that something perfect is 'more perfect' if it is actually real rather than imaginary seems to us (in modern days) a very unwarranted assumption. I reckon that many years ago it did not seem so odd.

More importantly, if we were to apply this logic to other ideas many people would find it laughable. Take Santa Claus for example (SPOILER ALERT!). Santa Claus is a fictitious character (hope you knew that already) that is a part of many cultures - at least, most of you who read this will think that. But I'm sure someone out there will claim that, in fact, Kris Kringle is as real as you and me, and he has amazing powers at Christmas time. You might say that that someone out there is crazy. Until that someone looks you in the eye and says "Santa Claus is perfect/the best/awesome at delivering gifts to everyone at Christmas time." By the logic laid forth above, Santa Claus must be real since the mere construction of the belief in this kind of perfection dictates its reality ... by definition! We have our tautology and with that, we can begin to imagine all sorts of crazy things into existence. Go ahead, try it! I've always wanted a pink-eared, fuzzy-bottomed, lion-tailed, ostrich-winged goldfish as a pet.

If you want a really great explanation/discussion of this ancient play on words, visit the skeptics guide to the universe and download podcast #80.

Now, if only I could find a politician who could even explain what the ontological argument IS, much less refute it, I would at least feel comforted knowing the intellectual capacity of the person running my government is better than a bush. If I cannot have a more skeptical candidate, at least I can have HOPE.

Fake Religion Fakery

Twenty-one days until the presidential election, and both campaigns are out in full force. Currently the news looks disheartening for McCain as he's seen a big drop in poll numbers recently:


Social conservatives don't like the fact that they are about to lose their hold on the American government and have been showing their distaste accordingly:

The incompetence is running amok this election year ... though I'm not inclined to believe it's ignorance any more. Citizens motivated enough towards political activism (in this case organizing, making posters, and protesting) generally check their facts before writing on the white board. Even a cursory glance at the news online or on television would indicate the fallacies of this protest poster. This sort of display is less an example of ignorance to the facts as much as it is intellectually dishonest about the facts ... a much more dangerous sin.

I believe FiveThirtyEight.com said it best, "Just to be clear, we at FiveThirtyEight are against Muslim-murdering Presidential Christian babies !FOR! Ohio." And I here at 'A Journey to Reason' blogspot am against intellectual dishonesty and the propagation of false ideas.

The marriage of Hitchens and ... Obama?

Worlds colliding for me today - Christopher Hitchens, one of my idols for critical thinking and independent inquiry, has just today endorsed the Obama-Biden ticket. While I agree with Hitchens in many realms, politics is not usually one of them as he considers himself a neo-conservative. One thing is for sure though; I may not agree with him, but his positions are very well thought out, intellectually honest, and defended with great vigor. I'm pleased to see that he is now supporting a candidate that I also believe to be the best choice.

His characterization of the McCain campaign's current predicament and national spotlight attention is quite keen:

Last week's so-called town-hall event showed Sen. John McCain to be someone suffering from an increasingly obvious and embarrassing deficit, both cognitive and physical. And the only public events that have so far featured his absurd choice of running mate have shown her to be a deceiving and unscrupulous woman utterly unversed in any of the needful political discourses but easily trained to utter preposterous lies and to appeal to the basest element of her audience.

Mr. Hitchens does not coat any argument with even the slightest bit of sugar. Here's what he has to say about Palin:

I wrote not long ago that it was not right to condescend to her just because of her provincial roots or her piety, let alone her slight flirtatiousness, but really her conduct since then has been a national disgrace. It turns out that none of her early claims to political courage was founded in fact, and it further turns out that some of the untested rumors about her—her vindictiveness in local quarrels, her bizarre religious and political affiliations—were very well-founded, indeed.

His arguments are pointed and frankly undeniable in most cases. The point with which I disagree is that he wishes the election could end post-haste as to save them more disgrace. I openly admit that I'd like to see this part of the campaign drag on - it's time for dirty campaign rhetoric to be exposed as the filthy manipulation that it is. With enough media attention to the non-sequiters and attack ads that McCain-Palin have hurled, I hope we could shore up enough embarrassment to last us at least two more elections in the future - maybe more.

The constant fear-mongering that is put out by the republican party must come to an end. Only when people realize that voting out of fear is not the best method to choose wisely will we be able to clearly rationalize a path into the future.

As for now - let the topsy-turvey worlds unite ... Christopher Hitchens for Obama!

Sarah Palin and the Dinosaurs

Well it's almost upon us ... the 2008 US presidential election is a mere 3 weeks or so away, and I can't wait for it to finish. It has been very exciting to follow, and at times, excruciating. For an update on where things stand, check out this awesome website where statistics are done right.

Sarah Palin (the current governor of Alaska) is McCain's pick for VP - and it's turning out to be the worst decision he ever made. In combination with the tanking economy, the McCain-Palin poll numbers have dropped to the point that some pundits are already calling the election for Obama-Biden. Only time will tell.

But why has McCain's pick not solidified a base and increased his numbers? Perhaps, in part, because middle america is worn out of religious fundamentalism that Bush has thrust upon us. Palin believes abortion should be illegal (including cases of rape and incest), beleves women should pay for their own rape kits, thinks creationism should be taught alongside evolution in the science classroom, believes that Iraq is a task from god, "tolerates" homosexuals and the choice they make, and believes in exorcisms (as she has had one herself) and speaking in tongues. This is just a sampling of the radical religious views Palin chooses to embrace.

Her lone media interview (with Katie Couric) was nearly unbearable - just to watch it I had to sit with my finger on the ON/OFF button because I just couldn't stand to hear her answers out of sheer embarrassment for her. How, in any way, did McCain think she was ready to be VP? One good thing that comes from this, is that she is a very inexperienced, fundamentally religious woman who has been thrust into the spotlight where she must answer to the scrutiny of the general public and mass media. Her fundamentally religious perspectives that are internally inconsistent are exposed in the national limelight. There have been times, that watching her answer a question with some religious rhetoric, she fumbles and almost seems to want to take it back, or change her answer - you can see her almost as if she realizes how stupid it sounds and she's about to change her view. Instead she continues to rattle it off, even though it just sounds utterly ridiculous.

This lame attempt to get peoples' votes by appealing to their religious/superstitious side is the case-in-point of how RELIGION is a very dangerous system. Most intelligent people I argue with about religion continue to rebut by saying, "But Matthew, who cares? At the end of the day, it's just a belief. Why do you care so much about what someone believes?" And my continual response is that it lays a foundation for someone to take absolute advantage of you. It never stops at 'just a belief in god.' There's always something attached - god thinks abortion is wrong, god created the world (he did not 'evolve' it), god guides our moral compass to attack other countries, god did not create marriage for homosexuals ... etc. Sarah Palin is using a dogma of superstition to connect with people and win their votes. It's despicable.

Of course she claims that her judgment is clear and that she is completely qualified to be not just the VP, but the Prez herself should John McCain pass away in office (which isn't hard to imagine seeing he's already 72 years old). Why should we questions her judgment? Aside from the fact that she says her foreign policy experience is sound because Alaska is right next to Russia on a map - the woman believes that dinosaurs lived with humans ... something science says couldn't have happened because we're separated by about 65,000,000 years of evolution.

Just remember - when you walk into the voting booth this November, ask yourself W.W.T.R.D.? (What Would Tyrannosaurus Rex Do?)

The XX --- XY divide ... evidence from Turner's patients.

I thought it would be fun to enter a science post ... and not just any science post, but something really cool and taken from about a decade ago. I work in a lab that focuses on mammalian sex determination, and there are many interesting debates that are tackled on a day-to-day basis. My boss brought this study to my attention earlier this month, and it was concerning research published in 1997.

David Skuse is very creative and wanted to find a way to see if there are differences in sex chromosomes depending on if we inherit them from mom or dad. In humans, two X chromosomes (XX) leads to female development, and an X and Y chromosome (XY) lead to male development. As such, when your parents used their gametes to make you, your mom HAD to pass on an X chromosome to you. If you are female, then dad happened to give you his X; alternatively, if you are male, then dad happened to give you his Y.

Well sometimes things don't go as planned, and instead of passing one of these on to you, a parent's gamete fails to deliver with any sex chromsome at all. Now, if you only receive a Y chromsome, you can't develop at all - the embryo can't survive. But if you only receive one X chromosome, you'll grow up just fine, though with a few minor problems. This scenario (45,X) is referred to as Turner's syndrome. These individuals, while only having one X chromsome, will develop physically as females. But interestingly, the single X chromosome could come from mom OR dad.

David Skuse saw this special group of individuals as a fantastic opportunity to explore some questions we have about human (and sexually dimorphic) behavior. In general, we think of girls as having better social cognitive function than boys. But could there be a genetic basis for this? The Y chromosome is very tiny in comparison to the X, so there are actually many genes that only exist on the X (which is important because you ALWAYS get two copies of every gene, one from mom and one from dad, unless you are a boy and only have one X). To keep things fairly at an equilibrium, girls actually INACTIVATE one of their X chromosomes so that they only use one, just like the boys - though this inactivation process is random. In the end, ALL boys use the X that their mom gave them, but girls use either the X from the mom or from the dad. This is where it gets interesting.

David Skuse hypothesized that maybe these X chromosomes are not the same - maybe they are partly responsible for different behaviors that we associate with the different sexes. He looked at Turner's syndrome patients and saw that some got their X from mom, while others got theirs from dad. He did a basic and thorough study to determine the social cognitive skills, comparing patients who got their X from mom directly to those who got their X from dad. His results are very interesting!


Subjects who received their X chromsome from the mom, scored much higher for social-cognitive DISFUNCTION! Individuals receiving their X chromsome from dad were much better adjusted and had better social-cognitive ratings. When compared to normal individuals, normaly XX girls have better social-cognitive skills than normal XY boys. This supports the notion that something on the X chromosome influences this behavior - XY boys have to get their X from the mom, and they do perform poorly, like the Turner's patients receiving the X from the mom. Alternatively, XX girls can use the X from either mom or dad, and they do much better with social-cognictive skills, like the Turner's patients receiveing the X from the dad.

This simple, yet elegant, study revealed the presence of an X-linked imprinted locus that affects social-cognitive skills in human sexually dimorphic behavior and supported the hypothesis of a genetic basis for this complex phenotype. Additionally, to quote the last sentence of the abstract, "If expressed only from the X chromosome of paternal origin, the existence of this locus could explain why 46,XY males (whose single X chromosome is maternal) are more vulnerable to developmental disorders of language and social cognition, such as autism, than are 46,XX females."

So remember, ladies - you have your fathers to thank (in part) for your superior social-cognitive skills. And guys, you can at least have the satisfaction of knowing that you'll be helping your daughter out, should you indeed 'decide' to pass on your X chromosome.

SUBMIT

Oh, it's that time of year again. School is beginning, new students are arriving, and for me the overcommitment begins. As part of my overcommitment to life, learning, and science, I'm co-chair of the Graduate Student Symposium committee. I'm also appointing myself to the marketing/advertising subcommittee.

As such, I've been working with my good buddy, Josh Lacsina. His ideas and acting together with my cinematography and production/editing skills, we've managed to put together a cool video. It also commemorates the 150th anniversary of the publication of 'On the Origin of Species' and the upcoming 200th birthday of Charles Darwin. This year's keynote address will be made by Dr. Robert Hazen, researcher at the Carnegie Institute who contributes to our understanding of origins research and early inorganic life.

Now, without further hubbub, the video. Be sure to comment and/or rate. Enjoy!