Glad to be an Ex

This is one of my favorite shorts from a new website called I am an Ex-Mormon:

I would love to see something like this expanded to more than just ex-Mormons. The world could use more examples of how happy (and moral) people are without religion.

Schumann Piano Concertos

Tonight Joey and I are headed to the San Francisco Symphony to hear the Schumann piano concertos. It starts at 8 so I'm going to stop blogging and go find my seat!

Moving Targets within a Cell

Anyone who has had an introductory molecular biology class knows that the genetic information for almost all living things (this idea gets trickier if you count viruses as living things) is stored in the form of DNA, or deoxyribonucleic acid. DNA is an elegantly simple, stable molecule that is a candidate for being the longest naturally occurring molecule on the planet (in your human cells, a single molecule of DNA would be two meters long if stretched from end to end – and that’s just from one cell!). From your introductory biology class you should also remember that, while DNA stores the genetic information, this information has to be turned into protein (the stuff that actually IS you) via an intermediate called RNA, or ribonucleic acid.

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!

SNOW OF THE DECADE!

Results of this study are pending:

NYTimes doesn't count on you reading carefully

These article listings came up on my NYTimes app today - the second one caught my attention:



The editors could have inserted stronger language in the Dickens subheading, considering that dead men don't normally visit talk shows, that is unless Oprah plans to go do some grave digging.

I'M NUMBER ONE!

My latest paper got accepted for publication in the journal Development and I'm pretty stoked about it - a lot of time, energy, sweat, and even a few tears went into my most recent manuscript. After publishing, every scientist hopes that their work will be noticed and cited throughout the field. You can always go check online and see how many times your paper has been cited, or whether or not your paper has been deposited in the pubmed database.

Well, today I got a very nice surprise, however temporary it may be. One of the hottest topics in cell biology today is turning a terminally differentiated cell (like a skin cell) into a pluripotent stem cell (like an embryonic stem cell), which can then be used to make any other cell type you want. It's a pretty powerful phenomenon that promises to revolutionize regenerative medicine. The process by which a differentiated cell reverts back to a more pluripotent state is referred to as reprogramming.

Imagine my delight when, after going to the pubmed database and typing in "reprogramming" to see what the latest and greatest reports are saying, my very own paper showed up! Take a look at this screenshot:

Here are two zoom pics if you can't see it:

That's my name there - Cook MS! Now, as cool as this is, my excitement is a bit tempered for two reasons:

1) In a day or two, when the next paper with the keyword "reprogramming" comes into the database, my paper will be kicked out of the number one spot. It will stay in the list for "reprogramming", but everything is listed in chronological order of publishing date.

2) The subject of my paper was not directly about turning differentiated cells into stem cells, nor did we (the authors) list "reprogramming" as a key word. The work is on a very related topic, but we do not include any direct reprogramming experiments - it seems as if the paper is listed because it has implications for and we discuss reprogramming. Still cool, but it's not as if we're changing a paradigm or anything.

However, for today I will revel in the knowledge that despite all of the research going on in the entire world about one of the hottest topics in stem cell biology, my paper is temporarily listed as number one in the pubmed research database associated with the term "reprogramming".

Woohoo!

Creationists and the 2nd law of Thermodynamics

On the upcoming 17th episode of the Pascals Bettors podcast, we have a Counter Creationism Corner where we discuss a common misconception that creationists put forth about evolution. A favorite claim by some creationists who try to dispute evolution is that “The second law of thermodynamics prohibits evolution”. Not surprisingly, creationists who claim this know just as little about thermodynamics as they do about evolution. Thomas Kindell, founder and president of Reasons for Faith Ministries, purports just such a claim that you can watch for yourself here - that is, if you can stomach even the first five minutes of it.

Most people don’t fully understand, and thus can’t question, the 2nd law of thermodynamics, but it has the allure of being one of the foundational tenets of a paradigm in physics, and people more readily question something that is referred to as a “theory of evolution” rather than a “law of thermodynamics”. The idea behind this argument is to present a seemingly longstanding scientific principle pertaining to a hard science, like physics, to topple the weaker, younger science of evolutionary theory. While this type of argument may have some emotional appeal, if creationists knew anything about the timelines of these two disciplines they would know why this is such a farce: Charles Darwin published his book, On the origin of Species, in 1859, but Darwin and others had put forth simple notions and publications about evolution much earlier. Although naturalistic thinking on biology dates back over 2600 years ago to the 6th century BCE with the greek philosopher Anaximander, proto-evolutionary ideas were set forth as early as 1745 by a few natural philosophers like Pierre Maupertuis, and later in 1796 by Erasmus Darwin, Charles Darwin's grandfather. Alternatively, thermodynamics emerged in the early to mid-1800s, largely due to the work of French physicist Nicolas Carnot, who believed that engine efficiency was the key to help France win the Napoleonic wars. It wasn’t until Lord Kelvin in 1854 that a concise definition of thermodynamics was recorded. Thus, even from the get-go, it seems that evolution has been around as long as, if not longer, than thermodynamics. BUT - this shouldn't matter anyways because it would be a logical fallacy to say that one science is more correct than another just because it has been around longer - so let's move on.

To begin our conversation about this topic, it is important to define our terms. Thermodynamics is the science of energy conversion involving heat and other forms of energy, most notably mechanical work. It turns out that, over time, several laws of thermodynamics have emerged. There are four well-known laws of thermodynamics: the zeroth, first, second, and third laws. The zeroth law is arguably the most fundamental of the four laws, but the need to state it explicitly was not understood until after the other laws had been formulated, in 1931. This law implies the definition of a temperature function, essentially demonstrating the possibility of constructing a thermometer. It is referred to as the zeroth because it is arguably the most fundamental of the four laws, but the need to state it explicitly was not understood until after the other laws had been formulated, in 1931. The first law (1850) is commonly expressed as the principle of the conservation of energy stating that the internal energy of an isolated system is constant - also commonly known as “energy cannot be created or destroyed” - this principle is at work in E=mc2, the equation that demonstrates the force of the atomic bomb, that matter and energy are interchangeable and the conversion of matter to energy is highly exothermic.

The second law (iterations in 1850, 1851, and 1909) states that heat cannot spontaneously flow from a colder location to a hotter location. This has to do with the universal principle of decay in the universe. The second law is an observation of the fact that over time, differences in temperature, pressure, and chemical potential tend to even out in a physical system that is isolated from the outside world. For example, this is how a space heater would work in your house - if you’re cold, you turn on the space heater - the heat produced in the heater is transferred to the air surrounding the heater which then increases in pressure and diffuses throughout the room until the air in the room produces a higher temperature equilibrium. As a result, you get warmer because the heat from the air is transferred to your body through contact. This is where it gets confusing. ENTROPY is a measure of how much this evening-out process has progressed, and entropy of a system not in equilibrium increases over time.

The word entropy is one of the most misunderstood concepts in thermodynamics, particularly by the creationists. It is a measure of the energy not available for work in a thermodynamic process. Think of it as diffusable heat in a room - the room itself is a closed system, until someone turns on a space heater - at this point, heat energy starts pouring in at one point in the room. According to the second law of thermodynamics, heat will transfer from the heater to the rest of the room. When the heater is turned off, the remaining heat will eventually diffuse and equilibrate throughout the entire room - as this happens, entropy increases until equilibrium is reached, at which point maximum entropy is recorded for the now closed system - but remember! This all changes if we turn the heater on again and create an open system with an outside input of energy.

The trouble with the word entropy comes in with its definition in the microscopic interpretation of statistical mechanics: entropy expresses the disorder or randomness of the constituents of a thermodynamic system. Unfortunately, many people walk away from this definition thinking that entropy = disorder on a macroscopic level. ENTER: the creationists! They think they are clever by saying “HA! You and I are complex and ordered! We could not have arisen through a process of evolution because the 2nd law of thermodynamics states that everything tends towards increased entropy, or disorder! HAHA!” This idea is absurd on its face for several reasons:

1) Disorder and entropy are not the same - the second law of thermodynamics deals with entropy. There are no laws about things tending to “break down”. There are no laws about disorder as people normally use the word. The 2nd law is about spontaneous heat flow or, more generally, about the impossibility to perform useful work indefinitely. The twists put on it by creationists, including “organized complexity” are entirely fictional.

2) All systems do not tend toward decay and disorder - on Earth, there are many systems besides evolution that tend toward greater order. Some examples are ice crystals and snowflakes, cloud formations, ripples in sand and water, cracks in drying mud, streams sorting stones based on size, growing plants when “left alone”, and the development of a human from a single cell. These are clear examples of order arising on Earth.

3) Complexity can form from simplicity - take the example of hurricane formation. This is based on the idea of a pan of water with heat applied uniformly to its bottom developing a convection current that is more complex than the still water. Complex planetary ring systems arise from simple laws of gravitation. Complex ant nests arise from simple behaviors. Complex organisms arise from simple seeds and embryos. A good mathematical example of this is the Mandelbrot set which describes fractals:

4) Earth is not a closed system - our planet is not an isolated system. There is a constant input of energy from the sun. Without the sun, it is clear that no life would be possible on our planet. Sunlight (with low entropy) shines on the earth, and heat (with higher entropy) radiates off. This flow of energy, and the change in entropy that accompanies it, can and will power local decreases in entropy on earth.

5) Even in a closed system, pockets of lower entropy can form if they are offset by increased entropy elsewhere in the system - the second law *does* apply universally (to our universe). But it allows for a local decrease in entropy to be offset by increases elsewhere. Intriguingly, the maximum entropy of a closed system of fixed volume is constant, but because the universe is expanding, its maximum entropy is ever increasing, giving ever more room for order to form. Cool, huh?

6) Increasing order is not a violation of the 2nd law, even temporarily. A violation would be a decrease in entropy without a greater increase in entropy to go with it. Neither growth or evolution violate the 2nd law because both take advantage of local differences in entropy to get work done. Evolution requires only reproduction, heritable variation, and natural selection - ALL OF THESE PROCESSES OBVIOUSLY OCCUR. THEREFORE, THERE IS NO VIOLATION OF THE 2ND LAW - if anything, the 2nd law would need to be re-written to accommodate the reality of evolution occurring.

In short, order from disorder happens on earth ALL THE TIME. Creationists who claim otherwise are either deluded or being intellectually dishonest. I'm not sure which of those is worse.

Pascal's Bettors #16

Hey Everyone!

A new podcast has been up since last week. Give it a listen!

The Perfect Gas Station

What is wrong with San Francisco? Besides all those other things you just thought of? I'll tell you - gas stations. I mean, the actual, physical setup of the structure and the odd amenities offered and not offered.

Ok, sure, there are plenty of wonderful attributes to this city I moved to almost two and a half months ago. But for all the fuss about reducing my carbon footprint and using public transit, sometimes I need to still drive my car to get to far away places or locations that public transit doesn't connect.

Besides, San Francisco is one of the most dense cities in the US - the streets are lined with cars that need to be taken care of and also need fuel.

Enter the confusing and inept world of SF gas stations.

Statement of disclosure: I have only been to four different stations in the city so far. I know an n=4 isn't great, but it's enough to get my complaints!

#1 why do you advertise the CASH price and not the credit? Because you want to trick me to your station, then laugh when I don't have cash. I never knew there was such a thing as gas CASH vs. gas CREDIT price. I had NEVER paid for gas with cash until I moved to this city. For those who don't know, the credit price is 30 cents more expensive PER GALLON!

#2 Why must you have payment "islands" instead of letting me pay at the fuel pump like every other gas station? Everyone must crowd around a central computing unit, and there are a surprising number of old ladies and foreign nationals that are confused by the endeavor.

#3 Why have a fee for using a debit card? Credit cards already charge me 30 cents extra PER GALLON! And if you don't have cash, you must pay a fee to use your debit card. Is this more incentive to pay with cash? Is there a big financial benefit for you to do this?

#4 Why do you have flat screen TVs at the pump but now towels or fluid so that I can wash my windshield? I thought that was one of the main staples at gas stations across the country - apparently not in San Francisco.

These are just a few of my frustrations in dealing with SF gas stations so far. If you have the answers to these, or any other quirky questions about gas stations on the left coast, please let me know. Otherwise, I will let you know when I find the first all-organic gas station. Oh, wait a minute...

Double the science, double the fun

Just inherited a nice PC monitor in my lab. Now I can do science TWICE as fast!