Friday, June 8, 2012

It might not be cancer...

Good job with the presentations on Thursday. Lots of fascinating stuff. Thanks for those who posted here and there's still time to do so if you didn't already. 

I'm personally taking a brief hiatus from posting (at least until summer session starts) and this particular blog will be going into hibernation until our new cohort starts up in the Fall. Feel free to check back in for a whole new fun year of blog posts for Introductory Biology in the Winter and Spring.

Fun story - I got home on Thursday and my dog is all over me, sniffing like crazy. Now he hasn't been trained to sniff out cancer but it was still a little alarming after hearing about that. Only after about 10 minutes did I find the slice of banana bread I'd forgotten in my pocket.

Sleeping > Studying ( some extent)

Good morning all! I hope your studying is going well - I thought that this article was particularly relevant to finals week. In brief, sleep is highly beneficial, possibly essential, for remembering things. You probably already know this - but seriously take it into consideration. Don't underestimate sleep, especially REM sleep. (If you're curious about the complex electrical signaling which causes sleep to help you remember things, the article is "Sleep to Remember" (Born, Rasch, and Gais 2006), which can be found here:

Do you need a place to live?

I stumbled upon an article a while back and you can take a look at their official site here:

They seem to have it fully planned out to send out a group of people to Mars by he year 2023, which if you think about it, isn't all that far away. They'll start out by sending a group of four people to "colonize" the planet, then every two years they'll send another four more people.

A co-founder said:  "By sending a new crew every two years, Mars will have a real, growing settlement of humans -- who would not like to follow that major event in human history?"
Personally, I wouldn't. And to me, that statement seems to actually mean: "There must be at least four people willing to go..."

The mission itself will provide us with invaluable scientific and social knowledge that will be accessible to everyone, not just an elite select few.

So... would you move to Mars? You know... for science?

Thursday, June 7, 2012

Oskar the Blind Cat

Here is the channel with videos of Oskar.

Some videos will show close ups of his face so you can really see that he actually has no eyes, but he can navigate pretty well without them.

Hummingbird Hovering

I thought this was a very good video about hummingbird flight. It is pretty amazing how hummingbirds have so much dexterity and maneuverability in the air. They can even fly backwards and upside down!

At about 1:35 scientists are performing the same experiment as in the paper I read, where they attach a string with weights on it to a hummingbird and see how many weights the hummingbird can lift.

If this link doesn't work, the video is called NATURE | Hummingbirds: Magic in the Air | Hovering | PBS

Natural Selection

Natural selection is fairly lazy, in my opinion, because it doesn't want to put energy into developing something new. If it absolutely has to create something new, though, it will do so at the expense of something else. Never will it just decide to make changes for the fun of it. For instance, we humans have five senses (sight, hearing, touch, taste, smell) and at one point during human evolution (approx. 23 mya), natural selection decided that trichromatic color vision would be very beneficial to humans. But because this would be such a huge expense (in time and energy spent), something else would have to be diminished. 

In one study, they found that the deterioration of the human olfactory repertoire was probably due to the development of trichromatic color vision. Olfactory receptor (OR) genes provide a basis for our sense of smell and human genomes possess more than 1,000 of these genes. But ~60% of these genes are pseudogenes, meaning that they are "turned off" and don't contribute to the phenotype. This is why we can't smell things as well as a dog. Most of dogs' OR genes are "turned on", allowing them to smell more things than we can.
Is there a reason why most OR genes are turned off in humans? The answer is yes, because natural selection does things for specific reasons, and for humans it seems to have deemed trichromatic color vision as more important than a great sense of smell.


So I took a class about oncogenesis (cancer growth), and we had been talking about possible causes for gene mutations. That is when I realized that nearly anything that is supposedly good for you (sunlight, legumes, sunscreen, wheat, etc) actually can cause gene mutations. And you can't simply say "well I'm just going to avoid these things altogether. That'll help me avoid cancer" because if you avoid sunlight altogether, you can become vitamin D deficient, which a lot of the population already is, or you can miss out on the benefits that certain food bring you. And realistically, avoid everything that could cause you to have oncogenic gene mutations would be basically to avoid life. Everything causes some kind of mutation. some mutations you are born with. I believe that basically, we all just need to realize that cancer is a likely thing to happen, and try to be as aware of it as possible to be able to catch it before it kills us.

 About the contagious cancer in tasmanian devils : It's caused by a virus which just so happen to insert its genetic code into a part of the host's genome which is too close to an important functional gene.

Wednesday, June 6, 2012

Lungless Frog

In class we learned about lungless salamanders. The only other four-limbed lungless creature is Barbourula kalimantanensis, the lungless frog! This species has been found on very few occasions. 
How does it get its oxygen, you ask? The frog respires through its skin and lives in cold waters, which hold more oxygen than warmer waters. It also has a low metabolic rate so it doesn't need as much oxygen. 

This article has more info on this badass little frog.

I was a rocket ship

TED is now getting into the education game - check out TEDEd.

There's not a huge amount there yet, just 85 videos compared to the TED site with over 900 talks, but it's new and I'm sure it will grow rapidly.

Tuesday, June 5, 2012

I found a pretty cool article related to my current research online that investigates the differing degrees of gene regulation of gene duplications in DNA-methylating species vs. those that do not methylate their DNA and how this causes differences in evolution of new gene functions of those respective species. I couldn't get the whole article to show up here, but here is the abstract:

Gene duplication is commonly regarded as the main evolutionary path toward the gain of a new function. However, even with gene duplication, there is a loss-versus-gain dilemma: most newly born duplicates degrade to pseudogenes, since degenerative mutations are much more frequent than advantageous ones. Thus, something additional seems to be needed to shift the loss versus gain equilibrium toward functional divergence. We suggest that epigenetic silencing of duplicates might play this role in evolution. This study began when we noticed in a previous publication (Lynch M, Conery JS [2000] Science 291:1151-1155) that the frequency of functional young gene duplicates is higher in organisms that have cytosine methylation (H. sapiens, M. musculus, and A. thaliana) than in organisms that do not have methylated genomes (S. cerevisiae, D. melanogaster, and C. elegans). We find that genome data analysis confirms the likelihood of much more efficient functional divergence of gene duplicates in mammals and plants than in yeast, nematode, and fly. We have also extended the classic model of gene duplication, in which newly duplicated genes have exactly the same expression pattern, to the case when they are epigenetically silenced in a tissue- and/or developmental stage-complementary manner. This exposes each of the duplicates to negative selection, thus protecting from "pseudogenization." Our analysis indicates that this kind of silencing (i) enhances evolution of duplicated genes to new functions, particularly in small populations, (ii) is quite consistent with the subfunctionalization model when degenerative but complementary mutations affect different subfunctions of the gene, and (iii) furthermore, may actually cooperate with the DDC (duplication-degeneration-complementation) process.

On a lighter note, here is a duck:

I've had an awesome time in the CCS Bio classes with you all, hopefully we will have a similar class in the future!
This is a pretty popular video that had spread around a while ago and it seems rather baffling. Legadema kills a mother baboon and while dragging its prey away, finds the baby of the baboon still alive. Seemingly, its maternal instincts kick in and out of curiosity or care, it takes care of the baby for the rest of the day not even caring about its previous kill. Was this a truly altruistic act imparted by a Leopard mother caring for the helpless or had it not a clue of what it was doing.  Whether it was raising it as its own or preparing it for a meal, no one will know as the baby baboon died over night.

Adverse reaction

Some fascinating research coming out at the moment on the potential negative effects of exercise. Since this goes counter to what we are all told such studies warrant close examination but certainly should not be simply dismissed because they don't fit the dominant paradigm.

First up, from the Mayo Clinic Proceedings this month: Potential Adverse Cardiovascular Effects From Excessive Endurance Exercise
where they review some of the evidence that long-term excessive endurance exercise can induce pathologic structural remodeling of the heart and large arteries.

Physically active people are much healthier than their sedentary counterparts. Exercise is one of the most important things you need to do on a daily basis,” he explains. “But what this paper points out is that a lot of people do not understand that the lion’s share of health benefits accrue at a relatively modest level. Extreme exercise is not really conducive to great cardiovascular health. Beyond 30-60 minutes per day, you reach a point of diminishing returns.

Second, and of more general relevance to the general population, a paper in PLoS ONE this week : Adverse Metabolic Response to Regular Exercise: Is It a Rare or Common Occurrence?

The review of six previous studies on exercise found that working out worsened at least one measure of heart risk — blood pressure, insulin level or levels of HDL cholesterol or triglycerides — for about 10% of people. About 7% of people declined on at least two measures.
For a scientist this doesn't seem that surprising after some reflection - although, on average, exercise may lead to a favorable outcome there may be a range of responses from individuals that span a range from very favorable all the way down to an unfavorable change.

Unfortunately I think you can imagine the headlines:
For those looking for an excuse to avoid exercise, here's one 
Can Exercise Actually Be Bad For You?
Exercise could be, er, bad for your heart, study says

Oh, and tomorrow is National Running Day...

Your inner fish

A repeat, but since Claudia mentioned it I thought I'd bump it up. I have the book sat in my office. If anyone wants to borrow it as long as you give it back so someone else can borrow it.

I just finished reading Neil Shubin's book 'Your Inner Fish.' It is a very easy and highly recommended read. We tend to focus on those areas where we have 'improved' on our fish-like ancestors (walking upright, doing pushups, inventing calculus etc) but what I found fascinating, and relevant to class today, was a discussion of olfaction (smelling) and how it's all been downhill since our aquatic past.

The human genome only contains about 23,000 protein-coding genes - which itself is an amazing fact. The other 98.5% of our genome consists of non-coding genes, regulatory sequences, introns and endogenous retrovirus sequences.

About 1,000 of those 23,000 protein-coding genes code for different odor receptors but less than half of them are functional in modern humans. Which says a lot about the importance of different senses in the evolution of humans from an aquatic ancestor (smell) to a terrestrial life (vision). Our evolutionary history is revealed in our genes.

Why Spinner Dolphins spin

The spinner dolphin is known for its incredible leaps out of the water during which they can spin up to seven times.  Until 2005 no studies should evidence explaining why the dolphins spun in the air, but it had been proposed that the spinning could possibly help with the removal of unwanted remoras.  In 2005 Frank E. Fish, Anthony J. Nicastro, and Daniel Weihs conducted an experiment that supported this hypothesis.  Using mathematical models they showed that spinning would be extremely helpful in the removal of remoras.

Normal jumping does not move the remoras because they are still parallel to the dolphins body causing them to feel minimum drag upon reentry into the water.  However, spinning causes the remora to become perpendicular to the dolphins body thus causing a significant increase in drag upon reentry.  This resulting drag is the force that dislodges the remora.

Monday, June 4, 2012

Strange Nervous System Adaptations in Reptiles

Strange Nervous System Adaptations in Reptiles

It is by coincidence that I am simultaneously learning about animal nervous systems in both this class and in herpetology.  I found out today that some reptiles, most notably the sea snake, can detect ultraviolet light through photoreceptors in their skin.  For the olive sea snake, the photoreceptors are present on the tail.  Sea snakes live in crevices in reefs, and cannot tell by plain sight or feel whether they are completely hidden from predators or not.  The ability to sense light with their tails lets them know that their tails are still exposed, prompting them to move them out of sight. It's almost like seeing with your skin!

Link to a related paper:

Little wing

This fossil insect wing (Stephanotypus schneideri) from the period about 300 million years ago when insects reached their greatest sizes, measures 19.5 centimeters (almost eight inches) long. The largest species of that time were even bigger, with wings 30 centimeters long. For comparison, the inset shows the wing of the largest dragonfly of the past 65 million years. (Credit: Photo by Wolfgang Zessin.)

Insects got bigger as oxygen levels rose during the late Carboniferous and early Permian. But around the end of the Jurassic and beginning of the Cretaceous period, about 150 million years ago, all of a sudden oxygen goes up but insect size goes down.

Blame the birds. In PNAS this week:

Environmental and biotic controls on the evolutionary history of insect body size.

Maximum insect size decreased even as atmospheric pO2 rose in the Early Cretaceous following the evolution and radiation of early birds, particularly as birds acquired adaptations that allowed more agile flight. A further decrease in maximum size during the Cenozoic may relate to the evolution of bats, the Cretaceous mass extinction, or further specialization of flying birds. The decoupling of insect size and atmospheric pO2 coincident with the radiation of birds suggests that biotic interactions, such as predation and competition, superseded oxygen as the most important constraint on maximum body size of the largest insects.
Tibetan Altitude Tolerance Mutations:

The people of Tibet, who have survived for thousands of years in extremely high altitude conditions, show distinct phenotypic adaptations to life in the mountains, of which the genetic basis is unknown.  Many groups, including mountain climbers, endurance athletes, and pharmaceutical companies, would love be able to use the evolutionary products of the Tibetan respiratory system to give other people an advantage at altitude.  This study scanned the genome of a sample of Tibetans and compared it to the genome of lower-elevation populations in the area, and analyzed where the two differ.  The two genes hypothesized to be most likely to contribute are EGLN1 and PPARA, which are known to be associated with the decreased hemoglobin phenotype expressed in Tibetans.  This study sheds light on the origin of Tibetan altitude tolerance, but more research is necessary to determine the exact pathway by which the phenotype is actually carried out.

Link to the paper:;329/5987/72

Sunday, June 3, 2012

Insect eyes

Here's a large collection of macro photographs of insect eyes and lots of other bugs and stuff.

Saturday, June 2, 2012

Communication is Key

Communication and contact are key to the preservation of a species. Despite this, humans have evolved to learn that the use of too many words can often make our intended messages unclear. Well, maybe its time we take things down a notch in communicational complexity and learn a lesson or two from Caenorhabditis elegans, a free-living nematode that knows how to get straight to the point when communicating with its peers.
C. elegans is used as a model system for understanding social behaviors such as foraging, population density sensing, mating and aggregation. Like many other eusocial species, C. elegans utilize the effectiveness of chemical signaling for efficient intra- and inter-specific interactions. However, unlike most eusocial species C. elegans has produced an assortment of 150 different chemical pheromones, which are secreted from the nematode’s skin, and can induce and prohibit specific behavioral activities among its fellow nematodes.
Recent observations and analyses have shown that C. elegans use small molecule signals – called indole ascarosides – to regulate behaviors such as population density sensing and mating. These indole ascarosides are able to receive input from two major metabolic pathways, amino acid catabolism and lipid beta-oxidation, which suggests that C. elegans communicate metabolic status through the use of a modular code of small molecule signals.

86 million year old lunch box

In a tenuous link to the previous posts on obesity I was drawn to the following news article on NPR:
Ancient Deep-Sea Bacteria Are In No Hurry To Eat

The Science paper the report is based on isn't quite as catchy:
Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay

 but the observations and the implications are pretty interesting:

They left the surface 86 million years ago with one lunch box, and they're still eating out of it. It's like they're splitting a pie, and they keep splitting in half and in half and in half, but nobody ever eats the last crumble. It's quite remarkable.
One reason scientists are interested in this extreme lifestyle is because it provides clues about the absolute minimum conditions required to sustain life. Andreas Teske, a marine microbiologist at the University of North Carolina, Chapel Hill, says that's useful for people looking beyond our planet for signs of life.

Friday, June 1, 2012

Thick and thin

If you played around with Framingham risk score calculator I posted yesterday you may have reached an erroneous conclusion. If you enter your age rather than  my age then you can enter some pretty unhealthy values for blood pressure and cholesterol and it still won't raise your ten year risk of heart disease much. It will probably still say <1%.

So does it not matter what you do? It's obesity - poor diet and lack of exercise that lead to high cholesterol and high blood pressure but if it doesn't raise your risk of death then why worry about it? Well the problem is that increasing evidence suggests that each year lived with obesity increases your chances of death (from both heat disease and cancer) way down the road -more than ten years down the road in your case. A recent study in the International Journal of Epidemiology actually quantified this: The number of years lived with obesity and the risk of all-cause and cause-specific mortality. Using data from, you guessed it, the Framingham heart study, they showed that the risk of dying increased 7% for every two years a person was obese, and for every ten years lived with obesity, the risk of heart disease and cancer mortality more than doubled. The researchers suggest counting "obese years" - similar to "pack years" for cigarette smokers - in order to better estimate health risks.