Looking Backward in Evolutionary Time

Researchers in Japan are studying how one monkey manages to see in the dark. Their work might change our entire perception of how the primate family tree evolved.

Most primate researchers agree that the common ancestor of today’s monkeys was nocturnal. Strangely, most modern primates are active during the day and have poor night vision. Azara’s owl monkey, which is active at night and has good night vision, is the notable exception.

This exception has led to a controversy  in the field. Primate researchers cannot seem to agree if all monkeys lost the ability to see at night before the ancestors of the owl monkey gained it back. On the other hand, it is possible that the ancestors of the owl monkey were just lucky; maybe they never lost the ability to see at night.

Enter Akihiko Koga and his team at Kyoto University in Japan. The Koga group are a team of geneticists who think that the owl monkey is in the process of gaining back the night vision that was lost by the early ancestors of today’s monkeys.

But peering back into time is hard to do. So Koga and his team needed a way to study if the owl monkeys are evolving better night vision or if they are already optimized for night sight.

They relied on a finding from another group that showed that the low light-sensing cells (rods) of the eyes of nocturnal animals package their DNA in a different way than most cells. Most cells keep gene-rich DNA in the center of the nucleus. This sets up a little hotspot for cellular machinery to get in and turn on genes. But the rods of nocturnal animals pack their gene-rich DNA around the edges of the nucleus. It seems like this DNA packaging pattern makes it easier for light to pass through the rod cell in nocturnal animals.

When Koga and his group looked at the rods of the owl monkey eye, they found that the DNA is packed in a manner that is halfway between that of nocturnal and daytime animals. This suggests that owl monkeys have decent night vision, but they probably are not the best at seeing in the dark.

The team still wanted to know if the owl monkey was on the evolutionary path to regaining night vision or if it had been stuck that way since the early nocturnal ancestor of primates. They found that a piece of repetitive DNA that is usually packed into the center of rod nuclei in nocturnal animals has been expanding like a virus into new locations throughout the owl monkey genome. This could explain how the DNA packing has been changing over evolutionary time in the owl monkey nuclei. Most importantly, it could mean that the monkeys are regaining the night vision that was lost by their ancestors. Maybe they are still evolving toward better night vision.

We are all just monkeys with bad night vision. It is interesting to think that we have some DNA lurking in us–because we share most of our DNA with our primate cousins–that has been co-opted in the owl monkey to bring back night vision. More importantly, this is a new way that biologists have been able to go against the grain of time and peer backward in evolution.

Image: Aotus Azarae by Rich Hoyer, Flickr

Mike Trout Talking to Umpires

He’s like your dad at a cook-out. Mike Trout just loves to stand around and shoot the shit with whoever happens to be around. Sometimes, that can be an umpire. Let’s take some time to appreciate Mike Trout talking to umpires.

(I don’t own any of these images; please see the accompanying photo credits.)

MLB: Los Angeles Angels at Toronto Blue Jays

“Very sorry, Mr. Trout. But that was strike three.”

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“I’m Mike fucking Trout, and don’t you forget it.”

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“So its like a picture of Spongebob, but he talks in a mix of capital and lowercase letters. What do you mean you don’t get it?”

Los Angeles Times

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“Did you guys see the last Game of Thrones? lol”

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“I know you’re just doing you’re job, man, but don’t you want to be on the right side of history?”

Phil Cuzzi

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Sometimes these interactions can turn downright violent.

MLB

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But who can stay mad at this guy?

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Thanks for reading this post! Give yourself a round of applause!

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Resistant Germs Beat Antibiotics to the Punch

Microbiologists reported that bacterial resistance to the antibiotic methicillin predates the use of the antibiotic in patients. This finding could underscore the need for entirely new types of antibiotics.

Methicillin, and its parent antibiotic penicillin, belong to a group of antibiotics that share a characteristic molecular structure. It was once widely used to treat Staphylococcus aureus infections, but resistance has since arisen and led to methicillin-resistant S. aureus (MRSA).

Researchers at the University of St. Andrew’s School of Medicine in the United Kingdom wanted to figure out when S. aureus became MRSA. They sequenced the genomes of 209 frozen samples of MRSA collected from patients going back to the 1960s. This allowed them to analyze minor genetic differences between the strains that researchers in the 1960s could only dream of.

The researchers found that strains from the 1960s contained genes that made them resistant to methicillin. Since methicillin was first used in patients in 1959, resistance would have had to develop soon afterward.

However, the team thought that methicillin resistance might have arisen earlier. When they compared the earlier MRSA strains, they found genetic differences between them that would have taken evolutionary time to develop. The simplest way to explain these differences was to conclude that the early MRSA strains shared a resistant ancestor that lived years before the introduction of methicillin.

Their estimates put the emergence of MRSA not long after the first use of penicillin, which debuted in the 1940s. The team concluded that widespread penicillin use led to the emergence of penicillin and methicillin resistance at around the time due to their similar molecular structures.

Today, tinkering with the same general structure to develop new antibiotics is a common practice. Studies like this highlight how we need to get more creative to maintain our upper hand on germs.

Image: S. aureus, from the CDC Public Health Image Library

Single Cells Seize the Means of (Food) Production

(Dinophysis acuminata. Photo credit: fjouenne, http://planktonnet.awi.de/)

Scientists reportedly discovered that an organism eats chloroplasts for breakfast…but doesn’t digest them until it has had the chance to use them first. The phenomenon might explain how the ancestor of all plant cells came to be over a billion years ago.

The study, published in the journal PLoS One, looked at single-celled organisms of the genus Dinophysis. Dinophysis species eat other single-celled organisms that contain chloroplasts, which are the green-pigment containing organelles that enable plants to make their own food from sunlight.

Usually, the story would end here; most organisms just digest up what they eat and that is the end of it. But researchers in the past noticed that sometimes Dinophysis does not immediately digest chloroplasts. Instead, it keeps them around.

This was an interesting observation because of an idea that is popular in biology that I will call the “endosymbiotic hypothesis.” The hypothesis is a proposed explanation for why complex cells–like human and plant cells–contain chloroplasts and/or mitochondria, while bacterial cells do not contain them.

The endosymbiotic hypothesis starts from the premise that chloroplasts and mitochondria–which make energy and food, respectively–look very much like bacteria. If you compare them under a microscope, they are around the same size. They grow and divide within our cells independently. They even contain their own DNA genomes that look like bacterial genomes.

The proposed conclusion is that simple cells that lacked chloroplasts and mitochondria could have eaten the bacterial ancestors of chloroplasts and mitochondria. Instead of digesting them, though, they could have just saved them to use as little energy factories.

This is a nice hypothesis, but to really buy it we would want to see single-celled organisms that can eat other organisms and then save their chloroplasts. So back to Dinophysis. Other scientists had already shown that Dinophysis can steal chloroplasts from their prey, but the team from Denmark wanted to track the chloroplasts in the Dinophysis cells over a long period of time. So they designed an experiment that involved growing Dinophysis in sea water and feeding them chloroplast-containing microorganisms and plenty of light. At a certain point, the researchers stopped the flow of microorganism prey but left the lights on. They did this for many days, and tracked the growth of the Dinophysis. Each time the number of Dinophysis in the sea water doubled, the scientists took a sample of them and looked at them under a microscope, taking note of the number and size of stolen chloroplasts remaining.

Keep in mind, the Dinophysis ate these chloroplasts. Based on that information, you would expect them to be digested before long. But we already knew that Dinophysis can keep the chloroplasts around for a while. The researchers were surprised, though: the chloroplasts were not just sticking around, but they were even growing and dividing in the Dinophysis! It was as though the chloroplasts had taken up residence in the Dinophysis and made it look like a plant cell.

Importantly, this is what we would expect to have happened at some point early in the evolution of complex cells. Remember, the endosymbiotic hypothesis predicts that there was once a single-celled organism that gobbled up the ancestors of chloroplasts and kept them around for a while to exploit them for a food source. The fact that we can see something like this happening in Dinophysis–and that the chloroplasts are even able to take up residence in their new host and start growing and dividing–adds evidence in favor of the endosymbiotic hypothesis.

This study does leave some unanswered questions, though. While the researchers showed some convincing evidence that Dinophysis is not digesting the chloroplasts and that the chloroplasts are in fact dividing over the course of weeks within their new hosts, they fail to show how this might be benefiting the Dinophysis. The endosymbiotic hypothesis predicts that the Dinophysis would gain a source of food from the new chloroplasts, but evidence of this in Dinophysis will have to come later.

In the meantime, this study could offer an interesting look back in time. We will never be able to turn the clock back on evolution, but experiments like this allow us to see how it may have proceeded all of those eons ago.

How the Eel Crossed the Atlantic

Anyone who has let their cat roam free over the neighborhood knows how keen a cat’s sense of direction can be. After all, they always find their way home–or so they saying goes. The European eel can do something quite similar, but its neighborhood stretches across the entire North Atlantic Ocean. Scientists are finally beginning to understand how these eels coordinate such a fantastic feat of navigation.

Scientists have long marveled over the young eels’ ability to find their way from their birthplace in the Sargasso Sea–off the coast of the southern United States–to the regions on the other side of the Atlantic where they spend most of their adult lives. They began to suspect that the eels, like plenty of other animals, use the earth’s magnetic field to navigate.

The earth’s churning hot metal core creates a magnetic field that surrounds our planet, providing practical benefits like protecting us from solar wind and allowing us to use a compass to figure out which direction is north. Some animals can even tap into this magnetic field to navigate, since each spot on earth’s surface is exposed to a different magnetic field due to its unique location between the earth’s poles.

Which leads us back to the eels. According to results published in the journal Current Biology, a group of researchers wanted to know how the eels would swim when exposed to different magnetic fields. To test this, they grew the eels in large tanks and exposed them to magnetic fields that would be characteristic of different geographic locations that the eels could occupy during their life cycle. Based on the results that they recorded in the tank, scientists could figure out how the eels would swim in the open ocean with a corresponding natural magnetic field.

Interestingly, this experiment showed that the magnetic fields would sweep the eels right into the Gulf Stream. We have all heard about the Gulf Stream, especially on the Weather Channel. In this context, though, the Gulf Stream is an ocean current that circulates around the North Atlantic in a clockwise direction.

The researchers concluded that the magnetic field would lead the young eels to the Gulf Stream, then the clockwise gyre of the Gulf Stream would lead them from the Sargasso Sea to Europe to spend their adult lives. Later in their lives, when it is time to return to the Sargasso to spawn, the eels would use the magnetic map to find the Gulf Stream again to return to where they started.

The researchers noted that this is the first evidence that eels use a magnetic map to coordinate their massive migrations, adding another species to the list of animals finding their way around earth with their very own internal compass.

Is the CRISPR Craze a Rerun?

Some years ago there was a basic science discovery that took the biomedical field by storm. Scientists working in a model organism had found a way to selectively target nucleic acids in the cell, shutting down gene expression. There was a ton of hype over the next several years, with everyone imagining the therapies that would start to help patients in no time.

You might think that I am talking about CRISPR; everyone else is, after all. But I am talking about RNAi, which was once touted as the discovery that would revolutionize medicine forever. I was talking to a colleague who is a bigwig in the CRISPR field who was speculating about the future of his field when he said something that shocked me at first. He suggested that CRISPR will not be the revolutionary clinical discovery that some people think it will turn out to be. When I pressed him, he compared it the hype behind RNAi a decade ago. Given this perspective, a couple of questions started to float around in my head. How similar was the hype behind RNAi to that of CRISPR/Cas9 today? Could CRISPR lead to the same letdown?

I did not know much about the RNAi craze–I know RNAi as a handy lab technique, but I never thought of it as a viable clinical treatment–so I went back and did some Googles. RNAi, which stands for “RNA interference,” is a set of cellular systems that cut up RNA and use the pieces to target and attack matching RNA transcripts in the cell. This turns down the expression of certain genes, which can be an effective way of doing genetic experiments in the lab.

It did not take much imagination to dream of how RNAi could be useful in treating human disease. Since plenty of diseases are due to the expression of disease-causing genes, doctors could treat the disease by giving the patient a drug to mobilize the RNAi system against the disease gene.

But in practice, RNAi ended up being difficult to use in patients. Hopes for RNAi therapy peaked during the mid 2000s, and started to ebb during the next few years after human trials showed no real benefit to patients or led to unintended immune responses.

Some people were afraid that RNAi would never live up to its promise. Biotechnology companies shuttered their RNAi research divisions. Human trials slowed down. Luckily, things did bounce back. There are still companies today working on RNAi therapies. It would seem that RNAi was over-hyped, it nearly crashed, then it became what it was always going to be: a therapy with some promise, but no miracle.

Today, CRISPR is just as hyped as RNAi was back then…if not more. CRISPR genome editing is popular science. In many ways, the lay public believes that this will be the century of biology: we will crack the mysteries of aging, we will edit human embryos to eliminate genetic disorders, we will cure all of the diseases. CRISPR genome editing is at the center of these hopes. But there are lessons to learn from the original breakthrough to end all breakthroughs. RNAi was not a complete failure, but we were certainly naive about its potential.

Part of what we got wrong was how unrealistic we were about the limitations of RNAi technology. Living cells have strong negative reactions to double-stranded RNA, which is a necessary step in the RNAi pathway. Delivery systems would be hard to engineer, just like the problems that still plague gene therapy. Finally, there is something that RNAi and CRISPR have in common: off-target effects.

Both RNAi and CRISPR depend on nucleic acids lining up and binding to each other in a pairwise manner before they can have their effect. Since the RNA sequences that bind to targets in RNAi and CRISPR are short and there is quite a bit of nucleic acid sequence in the cell, there is a possibility that you will get your molecule pairing up with an unintended target. It is like taking a short sentence fragment at random from a book and then searching the book for that fragment. You can find the target that you are looking for, but you might also find other perfect or near perfect matches elsewhere in the book, especially when you are searching through a large, complex book.

When these off-target effects happen with RNAi, you could shut down the expression of another gene. If that other gene is important, you might risk harming the cell. The same thing can happen with CRISPR. In fact, CRISPR has the potential to have more dire off-target effects:  CRISPR involves changing the DNA archive, rather than the RNA copy, which can lead to irrevocable changes to the cell.

Luckily, it does seem like CRISPR researchers have taken this to heart. Research into CRISPR’s off-target potential is an active field. I even blogged about a system that might be able to fine-tune the activity of CRISPR/Cas9 with the goal of reducing off-target effects in CRISPR therapy.

To be fair, CRISPR is at least a decade away from the clinic. But there are reasons to be concerned. Scientists have edited human embryos, and ethicists are scrambling to come up with rules to inform how we use this technology. If we learned anything from the RNAi experience, we should carry it over to CRISPR/Cas9. These systems seem to break out onto the scene with a ton of potential and bold claims. Eventually, we might be disappointed. There might be CRISPR trials somewhere down the road that will have to stop, with patients who thought they might be helped instead left wondering what all the hype was about. But if we have learned anything, it is that these systems will change our world. We will end up better off because of CRISPR. We just have to be willing to take the time to figure it out first.

Science Writing You Should Read

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I tweeted that a little while ago, and I really do try to live those words. Don’t tell my advisor, but I have been reading more popular science writing than actual research papers. But it can be pretty hard to know what to read. Where can a savvy consumer go for quality science writing? I’m here for you. Take these tips to heart.

New York Times

“The Gray Lady” has been a bastion of quality journalism for more than a century and a half. Fortunately, this includes the science coverage. The Times employs some great writers, including Carl Zimmer. You should start reading his work now if you have not already. In a world of science writers who just over-hype stories and don’t try to find holes, he is extremely skilled at getting all of the angles. If you want to read great, complex science stories, he is a great place to start.

Washington Post

Like the Times, this paper does great science writing in a newsy style. Their work tends to be a quicker read than the Times, and they print some quality stories. Check out Sarah Kaplan‘s work; she always has some interesting bylines.

The Guardian

Along with the Post and Times, the Guardian is also a newsy publication. The science coverage is always interesting, but I have detected a little sensationalism at times. It is nothing if not entertaining.

The Atlantic

Ed Yong might just be the best science writer doing it right now. Not only is his stuff great to read, but he also very accessible on social media (he favorited my tweet once). He is also extremely prolific, so check out his stuff on the Atlantic’s site.

Vox

Vox is a really cool online publication, where the writers always seem to be thinking just ahead of the curve. My new favorite science writer Brian Reznick writes for Vox, and I would encourage you to check out his work. He writes about anything, but he does seem to have a real interest in psychology and neuroscience. The rest of the science writers publish a ton of stories that will keep you reading throughout your workday.

FiveThirtyEight

I am a huge FiveThirtyEight fanboy. My heart stops every time I think I see Nate Silver on the street. Unfortunately, I have been a little disappointed with their science coverage. They just don’t publish that often…but what they do publish is pure gold. The main science writers, Maggie Koerth-Baker and Christie Aschwanden, are incredible. They also co-host a monthly science podcast in the FiveThirtyEightWhat’s the Point?” feed, if podcasts are more your thing.

Science

Science is usually regarded as a top research journal, but they have some great news writers. They will write up anything from their journal–or a competitor–as long as it is an interesting story. They do so accessibly enough for non-scientists to enjoy, but rigorously enough that scientists do not get bored. They also do some great writing on the intersection between science and politics, which is becoming a more and more interesting field in our current political moment.

Blogs
There are plenty of great blogs out there (just like this one). If you want to find some quality writing by people who just love to write about science, you should check out SciBlogHub or one of the other communities that compile and promote amateur science writing. Don’t forget to tell the writers what you think of their stuff. I know I love feedback, and I only wish I could get more of it.

RealClearScience

RealClearScience is just a page to point you toward the best science writing of the day. If you are just looking for someone to tell you what to read–and I’m busy or otherwise not responding on Twitter–just ask RealClearScience.

In the age of digital media, it is really not that hard to find science writing. Quality writing that is also accessible can be a stretch, though. But it is out there, and I will always be here seeking it out wherever I can–and trying to produce it, when I can. Let me know if you have any suggestions on publications that I missed. Happy readings.