Tuesday, April 25, 2017

Chaos! It's weird

So today in class when we were talking about chaos, I attempted to describe this gif:

It's pretty cool and illustrates lag pretty well. The top rod goes back and forth (duh) but the bottom rod lags behind and over compensates for the changes, leading to the cool pattern. According to wikipedia this is "one of the simplest dynamical systems that has chaotic solutions." The article has lots of math, but some other very cool visuals, some of which I do not understand.

Also this shell apparently looks like a representation of chaos called rule 30, which was developed by the guy behind Wolfram Alpha.  If you're looking for a fin Wikipedia hole to fall down, chaos theory is a good place to start.

Thursday, April 20, 2017

A BUNCH OF PALEONTOLOGISTS ARGUE OVER WHETHER OR NOT PROTOTAXITES WAS A GIANT FUNGUS OR A ROLL OF MOSS!!!!

Remember when we learned about that enigma fossil prototaxites? The one that maybe looked like a giant... well... it looked vaguely phallic. Some say it was actually a roll of liverwort moss. I'm skeptical of this, but the way I found these articles on the Web of Science is hilarious.

At the bottom of the page was this article:
http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=OneClickSearch&qid=29&SID=1F9ceq7GOkeWkpBd6Et&page=1&doc=10
with the title: STRUCTURAL, PHYSIOLOGICAL, AND STABLE CARBON ISOTOPIC EVIDENCE THAT THE ENIGMATIC PALEOZOIC FOSSIL PROTOTAXITES FORMED FROM ROLLED LIVERWORT MATS

Above that, was an article by the same people from later that year:
http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=OneClickSearch&qid=32&SID=1F9ceq7GOkeWkpBd6Et&page=1&doc=9
with the title:
ROLLED LIVERWORT MATS EXPLAIN MAJOR PROTOTAXITES FEATURES: RESPONSE TO COMMENTARIES

Directly above was an article from the SAME ISSUE AS THE LAST:
entitled: THE ENIGMATIC DEVONIAN FOSSIL PROTOTAXITES IS NOT A ROLLED-UP LIVERWORT MAT: COMMENT ON THE PAPER BY GRAHAM ET AL. (AJB 97: 268-275)

Wow. So much salt. 

Wednesday, April 19, 2017

CRISPR and Human Gene Therapy

Hey guys!
So this doesn't have as much to do with our current topics in the class, but I think it is a pretty important area of modern Biology (it was first discovered only in 2005) so I thought I would post about it (and it's kind of about biodiversity in bacteria and archaea).
I recently started working at the Arias lab that works in virology primarily with CRISPR-Cas9.
Many bacteria and archaea have a section of DNA known as CRISPR (Clustered regularly interspaced short palindromic repeats) that will produce RNA that will create a complex with a protein called Cas9. This complex is designed to find and cut apart foreign DNA from phages or plasmids and is a powerful form of defense for these organisms. Scientists have managed to develop our own versions of this complex; one of the most exciting parts of the CRISPR-Cas9 complex is that it can actually be engineered to cut out specific parts of a genome and then that area can be potentially replaced with whatever the scientist chooses. Our usage of this complex is not too advanced yet, but the potential for gene therapy and the ability to literally design a complex that can entirely cut out a genetic disorder in a developing baby is pretty huge. This is currently one of the primary contenders for gene therapy and it will be exciting to see how the technology develops in  the future.

Cool video explaining how it works


Tuesday, April 18, 2017

Endosymbiosis of the Powerhouse of the Cell

Does anyone else find it entertaining when you mention the mitochondrion during a discussion entirely in context and someone instinctively blurts out "mitochondria are the powerhouses of the cell"? Well, as we discussed just last week, they weren't always the powerhouses of eukaryotic cells. It turns out that the scientific community currently has more questions than answers about when, why, and how endosymbiosis most likely occurred.

Summary of this review paper, entitled "The origin and early evolution of mitochondria"

  • Organism with genetically "richest" mitochondrial genome (most likely resembles ancestral protist that underwent symbiosis) is called Reclinomonas americana
  • Like viruses, mitochondrial genomes underwent "reductive evolution," in which their genomes decreased in size by throwing out genetic information that was redundant within the host cell's genome
  • Genome sequencing alludes to the possibility that ALL mitochondria are derived from a single mitochondrion, meaning that this relationship arose only once in evolution
  • While it is not clear when exactly the mitochondrion entered the eukaryotic cell, the evidence is clear that they primarily evolved together to create the Eukarya domain
  • Mitchondria likely arose from a parasitic intracellular alpha-proteobacteria
While all of this is exciting, the evidence needs to be considered with a skeptical frame of mind. Much of the data to support the claims above came from genome sequencing, and the parts determined to be ancestral to the original mitochondrion may well just be ancestral to the universal common ancestor (for argument can be made that some of the genetic material in the mitochondrion that was considered in these studies have very far relatives in bacteria, archea, and eukarya).

So while it was an interesting read, and I think a lot was learned, not a lot was definitively claimed. But so is science.

Saturday, April 15, 2017

Since when was the tundra biome considered aesthetically pleasing?

I personally have never found the cold, barren plains of the tundra biome to be very beautiful, especially when compared to the others, such as chaparral (yep that's us! aka Santa Barbara, one of the most desirable places to live in the world). Last time I checked, people weren't jumping to pay millions of dollars for small houses on even smaller lots nestled in the most barren areas of Alaska or Canada or Russia...you get the point. However, contrary to my belief that the tundra biome could rarely be considered "aesthetically pleasing," a study in 2007 found that college students actually favor the tundra and coniferous forest biomes!! To be honest, I had to read that twice. Maybe my opinion is in the minority though, so what do you think? Is the tundra biome actually a gem?

http://journals.sagepub.com/doi/abs/10.1177/0013916506292016

Thursday, April 13, 2017

Octopusnuff part 2

The following paper may be inappropriate for people who think dolphins are kind and gentle creatures and/or people who really like octopuses and/or dolphins.

Things I did not know a few minutes ago:

1. Dolphins predate octopuses
2. There is a field of study called "prey handling" which is about how predators kill their prey
3. There have been observed cases where still kind of alive octopuses have suffocated dolphins trying to eat them.

Of course, there is some ecological analysis included about where (in more costal waters over sand, mud, and slit) and why dolphins are eating octopuses (likely because octopuses are the deadly kale of the marine world and because in the spring they are less equipped to fight back since they've been brooding).

And of course, this study took place in Australia.

Wednesday, April 12, 2017

Research/Outreach help

Hey everybody,
It just so happens that one of the labs I work in needs some peer reviews on harmful algal blooms and since we just recently went over dinoflagellates, and other types of phyto/zooplankton, I was hoping some of you could take some time to review our outreach materials! These are just drafts but we want to make sure it makes sense for someone who has limited knowledge on the subject. Email me at ddpunsal@gmail.com if you would like to help with reviews! Or you could just enjoy this poster...


Tuesday, April 11, 2017

Parasite Brain Manipulation

There's a cool book called "This is Your Brain on Parasites" that I never really finished reading. BUT today in class when we talked about the life cycle of that malaria causing organism, and how it has to move from the gut to the salivary gland of the mosquito, it reminded me of a story in the beginning of this book.  In this account, it describes how a trematode needs to first be in an ant and then in a sheep to mature, and how the trematode will basically take control of the ant's brain to make this happen. Unfortunately, I can't share the whole book, but I found an interview with the author, Kathleen McAuliffe, where she briefly describes this idea:

"Trematode are basically a parasitic worm, but they have three hosts often, or two hosts, different species, and there's a very interesting case of a trematode that when it gets into an ant's brain it instructs the ant to leave its colony at night and climb to the top of a blade of grass, lock on to it, and just hang there overnight. If nothing happens, it goes back down to the colony the next day and he returns the next evening and he will do that again and again until a sheep comes by and happens to eat that blade of grass with the ant attached, and when that happens the parasite gets into the sheep, specifically into its bile duct, which is exactly where it wants to be because that's the only place it can reproduce."

You can check out the rest of the interview here. And though I didn't finish the book, I would recommend it!

Saturday, April 8, 2017

Octopuses Rewrite Their RNA

I guess this discovery has been out for a few years now, but I recently learned that octopuses seem to have the ability to rewrite their RNA! This can be used for a lot of cool survival mechanisms, like individuals in polar environments changing neurons to function better in cold temperatures.
Here are a couple links:

  • http://www.sciencemag.org/news/2012/01/octopuses-rewrite-their-rna-beat-cold
  • http://science.sciencemag.org/content/335/6070/848

Friday, April 7, 2017

New Virus Discovery Sparks Debate Over Tree of Life

A newly discovered group of giant viruses, Klosneuviruses, may contradict our definition of viruses. Check out the article here.