Thursday, December 15, 2011
While in many places and to many people he is known for his literary and political writing and polemic, I have always loved him for his vigorous fight against superstitious believers. For some years now, it's been my dream to meet Christopher Hitchens - he fought tirelessly for human rights and for freedom from the tyranny of religion. He was a superb debater and had a wit matched by no one. It is sad to know that he is no longer with us to fight the good fight, but he lives on in his writing and in those of us who choose to carry the banner of science, skepticism, and critical thinking.
Almost every time I've seen a video of Hitchens he was smoking or having a stiff drink of whiskey. So tonight, this drink is for you. We'll miss you, Christopher.
Tuesday, December 13, 2011
Thursday, August 25, 2011
The geniuses over at Saturday Morning Breakfast Cereal webcomic have nailed it with a spoof on the well-known argument from design by the 18th century theologian William Paley. You can find the comic here, or see it below:
THE CHRISTIAN ARGUMENT: The world must be designed (by the Christian God). In the same way that you would look at a watch and clearly see all the parts could not have been made and put together by 'chance', so our world runs as intricate and perfectly as a watch, therefore there must be a designer (the Christian God, of course).
THE PROBLEM: The seemingly 'designed' world is full of sickness, death, oppression, tyranny, and disasters that do not discriminate based on race, sex, or religion. Horrible things seem to happen to people across all economic backgrounds and social classes. This indicates an indiscriminate God, a capricious deity, who randomly punishes humans for any whim. The only way this could be consistent with a deity that is also responsible for designing the world is if that deity is a dick. This is highly incompatible with a loving, personal Christian God.
THE ATHEIST RESOLUTION: Instead of supposing that there is a designer and that he's a dick (which is actually far more believable than the Christian version of a designer who actually cares about people), atheists simply (and correctly) challenge the notion that there is any interventionist, designer, or creator at all. It's not necessary, and our world does not need a creator. In fact, many have argued that the world is poorly designed in many ways, suggesting that there could not have been any overseer in the process.
Tuesday, August 23, 2011
Take this screen shot from one of the latest editions of the chart:
The Y-axis represents whether or not the evidence is strong for the supplement in question. By simply scrolling the mouse over the circle you can see what the target effect is - for example, in the image above, the evidence is strong that garlic is good for lowering blood pressure.
The size of the circle around the supplement ID represents its popularity in Google's search engine. Green tea, folic acid, and vitamin D show the most hits, whereas peppermint oil, devil's claw, and melatonin show the fewest hits. The cool color of these circles represents strong evidence - the brown color indicates that supplement does not have much evidence for or against it, and continued surveillance is important.
Now let's look at what didn't make the cut:
Well, well, well - royal jelly, despite the many late night TV ads that have been put out, is probably one of the biggest flavors of snake oil out there. It bottoms out along with wheat grass, chamomile, papain, and certain anti-oxidants for having no effect.
The next time you see a commercial promoting the ingredient of some supplement for a desired effect, check this chart out to verify the claim - most likely the commercial is over-reaching its claims, and could even be distorting the data. If you want to read the science, just click on the circle the website directs you to peer-reviewed published articles that support the claim or refute it.
It's good to be in the know.
Monday, August 22, 2011
Thursday, August 4, 2011
Thursday, July 28, 2011
Thursday, June 30, 2011
Theodicy is a theological or philosophical study which attempts to justify God's (largely in the monotheistic or Abrahamic sense) intrinsic (or foundational) nature of omni-benevolence (all loving), omniscience (all knowing) and omnipotence (all powerful), despite the existence of evil which, in the view of some, would otherwise stand to refute one or more of these qualities or God's existence altogether.SMBC posted this fantastic illustration of how most people are satisfied with these justification attempts and suggests why a more reality-based alternative to belief in god just doesn't fly with most people:
Monday, June 13, 2011
Sunday, June 12, 2011
PHD Movie Trailer from PHD Comics on Vimeo.
Looking forward to seeing this ... something's got to vindicate my decision to continue the grad student life as a postdoc ....
Thursday, June 9, 2011
Here's a preview of the upcoming documentary:
Thursday, June 2, 2011
Wednesday, June 1, 2011
In the city we went to the Golden Gate Bridge, Fort Point, the Exploratorium and Palace of Fine Arts, Tartine, Dolores Park, the Castro, Duboce Park, Alamo square, Golden Gate Park, the DeYoung Art Museum, Ocean Beach, Chinatown, Ferry Plaza, Fisherman's Wharf, Ghirardelli Square, the marina, Alcatraz, and much more. Outside the city we made it to Berkeley, the Marin Headlands, Sausalito, Muir Woods, and Sonoma. All of this in just under one week! We were pretty busy.
While the family was visiting, they became acquainted with our public transit system here called MUNI. Before their visit, I prepared by getting enough electronic commute cards, called Clipper cards:
Once the family arrived, they each received a card to get around in the city. It essentially costs $2 for two hours of riding on MUNI in the city, a pretty good deal if you strategize your trip well. I also didn't want them to lose track of *their* Clipper card, so I labelled the back of each one with a biology word that would stand out to them and that they could associate with their card in particular:
If someone ever stole it, there would be an easily identifiable marking too - handy especially considering that my credit card account is linked to those cards!
Do you know what each of those words means?
Friday, April 8, 2011
Wednesday, March 30, 2011
Thursday, March 10, 2011
We love getting feedback to, so use the "contact us" form on the website to let us know what you think and if you have any question or subject you'd like us to cover.
- Matt starts us off with Spreading the Bad News regarding the misconceptions about the Crusades
- Joel reads off some news items about the ACLU defending Christians, rape being declared as "God's Will" and another attempt to teach the bible in a public school
- Liz inspires us with some Words of Lizdom via Richard Dawkins
- John discusses an uplifting Church In State segment where the UK prioritized secular morality over religious hatred.
- Liz discusses some Pope-pourri, specifically a lawsuit german lawyers are using to take on the Pope
- Nik discusses the ethics of the Supreme Court's ruling in the Snyder v. Phelps case for the latest Ethics Corner
- Finally, we wrap up with a religious trivia question about the Jewish Mezuzah from Matt
Wednesday, March 9, 2011
What a terrible thing to do to the environment! I always thought that, aside from donating your body to science, cremation was the most cost-effective and ecologically friendly way to go (avoiding wood and metal coffins, large tracts of land, etc.). Well apparently there's a more environmentally friendly way to depart this mortal coil.
In short, a company called Promessa will freeze your body with liquid nitrogen (using no nasty embalming fluids) to the point that your frozen self becomes incredibly brittle. Then a sonicator is used to essentially vibrate the frozen stuff into a fine powder before evaporating the water in the dust and planting your remains back into the ground. The biggest environmental benefits appear to be no embalming fluid contamination, no inorganic burying material, and less space taken up. Here's a depiction from Promessa's website of the freezing process:
Wednesday, February 23, 2011
Tuesday, February 22, 2011
Monday, February 21, 2011
Did you hear? The House voted to bar Planned Parenthood from federal funding. They cut funding for HIV tests, cancer screenings, birth control, and more, putting millions of women and families at risk. We can't let it go unanswered. It's time for you and me to Stand with Planned Parenthood. Sign the open letter to the reps who voted for this bill - and to the senators who still have a chance to stop it. Don't just reblog: SIGN IT!I signed it - you should do it too! Maybe these sorts of petty funding battles wouldn't be so partisan if there were more women in Congress ...
Sunday, February 20, 2011
Simon Christen has produced a stop-motion video of the foggy city at different times of day and different seasons of the year. Check it out - it's pretty amazing:
Saturday, February 19, 2011
Friday, February 18, 2011
Thursday, February 17, 2011
You can actually go through all of the different options to decide what funding gets cut and what revenues get raised to balance the NC deficit. Give it a try! I cut 1.265 billion dollars of spending and raised 1.5 billion dollars in new revenue to give NC a surplus of 0.340 billion dollars. Of course, realistically, these decisions are much more complicated, but it's nice to see the options and have an idea of what sorts of financial cuts and gains are plausible. What can you do to fix the deficit?
Wednesday, February 16, 2011
History says that voters do not have the right to appeal. According to the Advocate:
Last month a three-judge panel for the ninth circuit asked the California Supreme Court whether Prop. 8 supporters who have defended the ballot initiative in the federal case Perry v. Schwarzenegger "possess either a particularized interest in the initiative's validity or the authority to assert the State's interest in the initiative's validity ... when the public officials charged with that duty refuse to do so."Fortunately the process is being expedited, but don't expect a decision on this matter any time soon. It seems that there is light on the horizon for the Prop 8 opponents - with a little more time, gay and lesbian couples will no longer be formally discriminating against by the government. Better late than never.
In other news, the Hawai'i legislature approved civil unions today for same-sex couples, and the Governor plans to sign the bill. This brings the tally up to 10 states that offer domestic partnership and 5 states plus Washington DC that allow same-sex marriage. It's a long road, but we'll get there eventually.
Friday, February 11, 2011
Thursday, February 10, 2011
Wednesday, February 9, 2011
Until then, take a look at this MRI image of a glioma taken from the Mayfield Clinic website:
Tuesday, February 8, 2011
I give you, Evolution Made Us All, by Ben Hillman:
Evolution Made Us All from Ben Hillman on Vimeo.
Monday, February 7, 2011
Well here's something else Christians may have trouble explaining - a simple graph depicting the number of murders that occur in the Bible committed by either God or Satan:
Information originally shared from a StumbleUpon post.
UPDATE: For clarification, the SumbleUpon post was referred to me by the noble Greg Barnes, otherwise known as Greggles.
Saturday, February 5, 2011
Reason has long been the bane of the theologian's existence - constantly prodding; questioning; forcing religious leaders to re-think their magical explanations because, as it turns out, there's a natural force that seems to be lurking behind anything at which we turn our microscopes or telescopes. Although it can sometimes seem that the religious kooks that *you* have to deal with every day are the most zeus-awful ignoramuses that ever existed, take solace in knowing that ignorant and inflammatory religious figures are nothing new - religion has been practicing their aversion to critical thinking for quite sometime. In fact, one of the most well-known religious leaders, the one who provided the intellectual and emotional vigor for splitting off from the Catholic faith and creating what we know today as Protestantism, spewed some of the most ignorant and vile stupidness long before we had Jerry Falwell or Pat Robertson. I give you the infamous words of Martin Luther, from Works, the Erlanger Edition v. 16, p142-148:
Reason is the Devil’s greatest whore; by nature and manner of being she is a noxious whore; she is a prostitute, the Devil’s appointed whore; whore eaten by scab and leprosy who ought to be trodden under foot and destroyed, she and her wisdom… Throw dung in her face to make her ugly. She is and she ought to be drowned in baptism… She would deserve, the wretch, to be banished to the filthiest place in the house, to the closets.Doesn't that just make you proud to be a protestant?! And know that this sort of misguided thinking is not out of an unbiased evaluation of the concept of critical thinking or reason. Martin Luther had a clear agenda:
Reason is the greatest enemy that faith has; it never comes to the aid of spiritual things, but—more frequently than not—struggles against the divine Word, treating with contempt all that emanates from God.Aren't you happy that we don't live in the early 1500s, with Martin Luther as a King? Imagine if he were alive today ... he would burn us all at the stake because of our acceptance of the internet, vaccines, and goodness knows the gays!
Friday, February 4, 2011
Of course, conservatives also like to turn our current president, Barack Obama, into a scary Marxist monster. Conservatives have accused Obama of being too dark-skinned/muslim (the same thing in conservative speak), too socialist, too peace-making, and wanting to "give" away healthcare to the poor. Religious politicians from the right have attempted character assassination, implying redistribution of wealth and universal healthcare to be terrible ideals ... of course, they think they know what Jesus would do. This picture pretty much summarizes my thoughts on the matter:
Thursday, February 3, 2011
Wednesday, February 2, 2011
Tuesday, February 1, 2011
This time they're excluding gay couples from a counseling camp in Rome, Georgia. Chik-Fil-A funds the WinShape foundation which sponsors couples retreats for both unwed and married couples.
The foundation was asked if gay couples could attend and their response was (via Good as you Blog):
"WinShape Retreat defines marriage from the Biblical standard as being between one man and one woman. Groups/individuals are welcome who offer wholesome, educational conferences and programs that are compatible with Biblical values and WinShape's purpose."In a follow up response Chik-Fil-A directly indicated that they do not accept homosexual couples at the retreat according to their contract.
Surprise, surprise: a Christian funded group is excluding gays from their couples oriented activities. Which part of this is "hate the sin, not the sinner" mentality that I grew up with in the South? Besides, Jesus never had a girlfriend. And we all know that a man who's in his thirties but has never gotten laid is probably as gay as the day is long - especially if he wasn't laid by age thirty in the year 30 BCE, when people were marrying at age 12. I know that god must have a soft-spot for gays anyhow - King David, one of god's favorites, had a raging hard-on for Jonathon for like half of the old testament. Plus, god makes rainbows. Ergo, god is gay.
So, biblical standard is what is important, right? Chik-Fil-A wants to keep gay couples out because the bible says so? Then maybe they should stop and think about whether or not they should abide by any more of the rules set forth in the old testament (or New Testament for that matter). I bet they would let divorced couples attend the meeting - and it's clear that divorce is frowned upon.
But of course Chik-Fil-A doesn't care about this because their reasoning is not sound - it's just an excuse to bolster their own cultural discomfort in failing to understand something that's foreign to them. You could try to reason with them, but I have learned in my old 27-years of existence that you're best not to do that: you can't reason someone out of something that they didn't reason themselves into in the first place.
Monday, January 31, 2011
Saturday, January 29, 2011
Normally doctors try to keep your blood stream clean of cholesterol – otherwise you might get a clot that will stop the blood flow and kill you. In this case, the doctors reckoned that they could induce an artificial clot (called an embolism) right at the site of the artery branching off to the tumor to block the blood flow and attempt to choke it off from oxygen and food – this way, when they ressect the tumor there would be less risk of bleeding. So, they used a commercial product called Gelitaspon (small gelatin sponges) and injected some in the artery leading into the tumor. You can see here that this successfully reduced the blood flow to the teratoma:
Friday, January 28, 2011
Thursday, January 27, 2011
Wednesday, January 26, 2011
Tuesday, January 25, 2011
Monday, January 24, 2011
Sunday, January 23, 2011
Friday, January 7, 2011
Thursday, January 6, 2011
That one little “deoxy” difference between DNA and RNA makes RNA a very dynamic (and frequently unstable) molecule. In chemical terms, “deoxy” is referring to the lack of an Oxygen atom (or hydroxyl group) in DNA that is present on RNA:
Oxygen, if you don’t already know from principles of how a fire burns, is a very reactive species in the chemical world, so it makes sense that the presence of an extra oxygen atom in the RNA molecule makes it more unstable than DNA. However, the dynamic nature of RNA makes it really handy for all kinds of other chemical reactions and cellular processes – another way to say “unstable” is to just say “reactive”; and in your cells, millions of chemical reactions take place all the time, so a reactive RNA is really useful. In fact, it turns out that your cells can regulate on a finer scale whether a gene is turned on or off at the RNA level than at the DNA level.
Think about it: if you want to turn a gene on (genes are made of DNA), you need to get all the molecules situated just right over the gene so that it can make copies in its intermediate form of a particular kind of RNA called messenger RNA, or mRNA. Those mRNA copies can then go out of the nucleus into the rest of the cell and be turned into protein. Of course, you only have two copies of a gene in your cell, a pitifully small number. How can you make billions of copies of a protein from only two copies of DNA? Well, your cell makes thousands of mRNA copies of the DNA gene. Those thousands of copies of mRNA go out into the cell and are used by other molecules to make protein – usually, one mRNA copy is read over and over again to make lots of protein, and that’s how you get millions of copies of a single protein in a short amount of time.
When a cell is done making and using this protein, it can go down to the DNA to “shut off” the gene by removing all those molecules that are making mRNA copies, which will in turn keep any new protein from being made. That is, as long as the mRNA copies that are already present simply go away once the DNA gene stops making them.
But what exactly happens to an mRNA copy after the DNA gene is turned off? Does it just degrade and disappear? Can it linger around? Can it be “turned on” and “turned off” like a DNA gene can? These are all questions that people who work on RNA biology have been asking for quite some time, and the answers can be pretty amazing and pretty complex.
While other classic research has shown that mRNA copies can hang around and be turned “on” or “off” regardless of what’s happening to the DNA gene, a study published in 2007 showed some pretty cool results demonstrating that RNA copies can be trafficked around inside a cell by riding along one of the biggest structural proteins inside a cell: microtubules.
Michael Blower at Harvard University, in collaboration with Karsten Weis and Rebecca Heald at UC Berkeley showed unambiguously that mRNA copies can bind to microtubules and play an important role in localizing their protein products to a specific site within the cell. As you can imagine, trying to get enough molecules to do experiments can be hard sometimes, especially if you have to do all your experiments from a single cell. However, scientists have clever ways to amplify material, and they have a habit of studying animal models that have REALLY big cells to make this easier. This is where females from Xenopus laevis, or frog, come into the picture. Xenopus females lay incredibly large eggs (an order of magnitude bigger than human eggs) and in very large numbers (400-500 at a time!). Blower and colleagues used these massive cells to extract and purify allll the microtubules (MTs) from the rest of the cell – what they found is that there are mRNA copies stuck to the MTs!
This graph is showing you all of the mRNA copies in the Xenopus eggs and whether they are bound to MTs or not. The X-axis is showing you “enrichment on MTs” and the higher the number, the more it’s enriched. The Y-axis is showing how many mRNA copies are enriched at that amount. For example, there are 140-160 mRNA copies that are approximately -1.4 Log2 enriched, and only 5-10 mRNA copies that are about 1.3 Log2 enriched. Notice that a lot of the transcripts are not enriched; in fact, they’re in the negative numbers indicating that they aren’t found on MTs but elsewhere in the cell (makes sense). However, a select few mRNA copies are actually enriched. Fortunately, the experiment that gave them this pretty graph also gave them the identities of each and every one of those mRNA copies.
So they did the next logical thing: if one experiment suggests that certain mRNA copies are stuck on MTs, then this should be visible in the cell. They decided to check it out using a microscope by labeling an mRNA and MTs to see if they look stuck on each other (the scientific word for “stuck on each other” is “overlap”). Don’t you worry about how they labeled it – that’ll be an entry for another blog post some time.
The red color indicates MTs and the green color indicates potential mRNA copies that should overlap (blue represents the DNA, but just ignore that for now). Notice that the left two panels show green mRNA copies that actually do overlap in the same region as the red MTs – this is exciting and confirms their finding. On the right you see a negative control – or an mRNA copy (called net1) that should NOT bind MTs, and indeed you don’t see any green staining, do you?
This is really cool, but the people who gave these researchers money to do research are … well, they’re taxpayers! And taxpayer money (funneled through the National Institutes of Health, or NIH) means that there’s usually a pretty strong interest in human experiments, not frog experiments. So the next question was, “If this happens in frogs, can it happen in humans?” And that’s exactly what they checked – so they took some human cells that grow in culture (no human eggs or anything like that, just human body cells), purified allllll the MTs away from the other stuff, and did the same initial experiment:
Notice again that a few mRNA copies are enriched on MTs, but most are not. This is a pretty cool idea: the same thing that can happen in frog eggs is going on in human cells too! But why would mRNA copies want to be on MTs? If mRNA copies are located on MTs, does that mean protein is made on the MTs as well? The process of reading mRNAs and making protein from them is called translation. So the scientists in this paper performed an experiment to test whether translation (the process of making protein from mRNA copies) is occurring on MTs. A clever system was adopted from previous work devising a method of labeling sites of active translation with a derivative of the antibiotic puromycin. Puromycin kills cells by getting lodged into the molecular machinery that turns mRNA copies into protein. So scientists made a version of puromycin that is tagged with a fluorescent molecule to see under a microscope. By injecting small amounts of this glowing puromycin into cells, it lodged itself into molecules called ribosomes, and labeled active sites of translation (such small amounts were injected that cell death was not a concern):
It worked! And it appears that translation is occurring on MTs. Notice the green puromycin in the left panel, which labels active translation, overlaps with the red color labeling the microtubules. You'll also note that it seems to be concentrated green at the tips of the red staining. That area is called the spindle pole, and the right panel shows a different green marker, ribosomes. Ribosomes are the molecular machinery that promote translation of mRNA copies into protein. So translation machinery is located on the MTs and at the spindle poles, and we know that active translation is occurring on MTs because the puromycin stains it too!
This is a pretty clever trick to answer their question, and they also proceeded to show that the same phenomenon occurs on MTs in meiosis as well as mitosis (remember that meiosis is cell division of the sex cells in your body, but mitosis is cell division of the rest of the cells in your body - the focus is on cell division because that's when lots of MTs organize to form really clear structures that you can look at). The last question they attempted to address was, “Is the process of translation necessary to move the mRNA copies to the MTs?” This is more important of a question to answer than you realize, but it is difficult to know what is responsible for moving mRNAs around a cell.
One hypothesis is that the translation machinery moves mRNA copies to MTs, so that’s one of the easier questions to answer. This time, the experiment required a bigger dose of purmocyin to stop the process of translation altogether. If translation is stopped altogether, then the mRNA copies may or may not be located on the MTs. The results are below:
The microtubules are in red and the mRNAs are in green. The top row is normal cells and the bottom row shows cells treated with the translation inhibitor puromycin – notice that the green mRNA copies still localize to the MTs even when translation is inhibited with puromycin in the bottom row.
These experiments, among others, make this a great paper. However, there are many questions that are left unanswered. Why are some mRNA copies localized to MTs but not others? What molecules and processes are responsible for bringing the mRNA copies to the MTs? If the mRNA copies are not allowed to localize to the MTs, will something bad happen? You can easily see how the experiments for the next possible paper are shaping up.
If you found these results interesting, you might also like this incredible video made at Harvard, animating the life of a cell. In it, you’ll see one depiction of how scientists currently think mRNA copies and other cargos are moved along microtubules (to some pretty awesome music no less).
Stay tuned for more science next week!