The Curious J: A science blog

Exploring life, one atom at a time.


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Genetic Engineering Pt. II: Tools of the Trade

As introduced in my previous post, this is the second of a 3-part series on genetic engineering. The first post was a brief overview and introduction to genetic engineering; while this one will focus on the tools used, and explain the difference between artificial selection and genetic modification. The third and final post will cover some of the more controversial topics, such as personalized medicine and genetically modified organisms (GMOs).

Artificial Selection: How We Created Man’s Best Friend

In order to explain the differences between genetic modification and artificial selection, it’s easiest to look at specific examples. A prominent example of artificial selection is the animal that has touched so many hearts it’s been named “man’s best friend”- dogs. Dogs are especially interesting because they are believed to be the first animal ever domesticated, occurring even before agricultural animals such as cattle, and there are now several studies suggesting that dogs were independently domesticated  twice.

All dog breeds come from a common ancestor – the gray wolf. Genetic sequencing studies show how closely they are related. So how exactly did we get the chihuahua from the gray wolf? Through thousands of years of selective breeding, even as long as 30,000 years. Let’s start with the gray wolf meeting humans: it’s unknown whether humans sought out a relationship with wolves, if it was vise versa, or if it was a mutual “agreement”. However it happened, humans began to interact with wolves to the point where they were breeding them for specific qualities.

From the beginning of domestication, people recognized that if you cross two wolves that are docile than their offspring will have a high chance of being docile as well (versus breeding more aggressive wolves). If you continue this process, while also eliminating the aggressive wolves – let’s be honest, this occurred – than you would eventually, through several generations, have only docile wolves. If you continue this process while concentrating on a single characteristic at a time, such as size or coat-thickness, than eventually the wolves become so genetically different from their descendants that they became a new species: dogs.

For dogs, several characteristics were altered over thousands of years by repeatedly altering a trait at a time. In more modern times, such as with cattle and other agricultural animals, only a single trait or small set of traits is targeted for alteration, not allowing for speciation, or the separation of one species into two.

This same process is used for the domestication of plants. Although the exact date when wheat was first domesticated is still debated today, it is known that the wheat we consume today varies genetically from wild wheat due to years of selective breeding. Two traits in particular allowed humans to consume and to grow wheat: an increase in grain size and the development of non-shattering seeds. The former allows for easier cultivation of the seedlings and the latter prevents natural seed dispersal, so that humans can harvest the seeds at the optimal time. It’s believed that both of these traits occurred naturally, and humans took advantage of them by only selecting for plants with those qualities. Today, common wheat differs even greater from the wild ancestor through actual breeding programs. Wheat breeding programs around the world have artificially selected for traits that mostly confer a resistance to either a pest, disease or other environmental factor, creating a much more modern version of wheat.

For a further understanding of artificial selection, check out these links:

Genetic Modification: The Simple-ish Version

As mentioned in my previous post, genetic engineering, or modification, has been in practice since the 1970’s, when Boyer and Cohen first successfully recombined DNA into E. coli. Although the procedure Boyer and Cohen used, known as recombinant DNA technology, is still used today along with several other methods, there is a current shift into using CRISPR technology as the main tool for genetic alteration. Since this shift is occurring and there has been a focus on CRISPR, both by those that support genetic engineering and those that don’t, the rest of this post will have a major emphasis on CRISPR technology.

CRISPR stands for Clustered Regularly Inter-spaced Short Palindromic Repeats. Palindromic repeats are prokaryotic DNA containing short repetitions of base sequences, and in between the sequences are short segments of non-coding DNA (“spacer DNA”). One of the main components of CRISPR technology are CRISPR associated proteins, or Cas proteins, which are endonuclease enzymes – enzymes that will cut double-stranded DNA (dsDNA) – that are guided by RNA. CRISPR and Cas proteins are naturally found in several species of bacteria, and work as mechanisms of immunity by cleaving the DNA of invading pathogens, such as viruses. Although there are multiple Cas proteins, the Cas9 endonuclease found in Streptococcus pyogenes is currently the most efficient Cas protein, thus the current technology is known as CRISPR/Cas9. 

CRISPR/Cas9 technology is progressively getting more complicated with the addition of new information and modifications to the current methodology. However, the basic procedure that CRISPR/Cas9 performs remains the same. As mentioned, one of the main components of the technology is the Cas9 protein. The other component is a guiding RNA (gRNA). The gRNA is created so that it matches, or compliments, a DNA sequence within a genome. The gRNA will find that sequence and will hybridize to it. Next, the Cas9 protein uses that gRNA as a guide to find and bind to both the gRNA and to the DNA it’s hybridized to – binding to both strands of the DNA, not just the strand the gRNA is hybridized to. Finally, Cas9 will cleave both strands of the DNA. When the dsDNA is cleaved, the cell will detect there is a cut and when repairing the area, mutations will be introduced in a natural repair process. If the DNA encoded a gene, the introduction of a mutation will alter or silence the expression of that gene.

crspr_cas9

 

After gaining an idea of what the CRISPR/Cas9 system does, it makes sense that scientists are trying to use this tool as a way to silence and edit genes. The system can be modified to target specific genes by creating specific sequences of gRNA. Current studies are using the system in several new ways, including studying epigenetics – the study of how gene expression is effected by the environment, and the potential to target genes associated with cancer and Alzheimer’s, among other diseases. The first cancer-targeted CRISPR human trial has been green-lighted by the National Institute of Health, and may mark the beginning of a future where diseases are edited out of the genome.

Stick around for the next post, I’ll be covering further controversies associated with gene editing. And if you would like any further information on CRISPR/Cas9 technology, please check out the following links:

 

Author’s note: in an attempt to reach a wider audience, the processes of both artificial selection and genetic modification have been simplified. Before forming any opinions of either subject, I highly recommend doing further research on both topics. Thank you for reading. 

 

 

 


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The Invisible World of Microorganisms

As humans, it’s difficult to imagine the world in a scale that is different than our own, especially when that difference is significant, such as the expanse of the universe or the workings of a cell. That’s what makes microorganisms so interesting. There is an entire world among us and in us that is invisible to the naked eye. Now, not only are we aware of these hidden communities, but we use microorganisms in a wide range of industries, and we also know that the bacterial communities living inside and on us help keep us healthy. With all of this unseen activity among us, learning about microorganisms opens up our eyes and minds to an once-invisible world.

What is a microorganism anyway? 

The simplest definition of a microorganism, or microbe, is an organism that is too small to be seen by human vision, i.e. can only be seen with a microscope. Of course, microbes are much more complex and diverse than this definition implies. First off, microbes can be single-celled organisms or multicellular, and there are several categories of microbes: bacteria, archaea, fungi (includes yeasts, molds, and mushrooms), protista (algae and protozoa), and viruses.

Bacteria:
E. coli

Escherichia coli 
Archaea:
archaea
Pyrococcus furiosus
Fungi:
Fungi
Zygomycota rhizopus
Protista:
protista

Noctiluca scintillans
(Sea Sparkle; protozoa)
Viruses: 
Virus
Orthomyxovirus (Influenza)

Viruses are especially interesting in that it has long been debated whether viruses are “living” organisms are not, since they lack one of the seven characteristics of life: the ability to reproduce on their own [1]. Viruses need cells from other organisms in order to replicate, or reproduce. That is also why they are considered such a threat to our health—they can move from cell to cell, replicating and usually killing the cells they inhabited along the way. As I’ll soon discuss though, viruses can also be used for good.

Microbes are actually everywhere

Microbes can be found in any type of environment, including the human body. Since they can be found virtually everywhere, I’m only going to describe the more extreme habitats. Microbes living in these conditions are known as extremophilesTo start with, microbes can be found in the deepest parts of the ocean. When divers first discovered hydrothermal vents at the bottom of the ocean, they were surprised to find thriving communities of life there [2]. It turns out that microbes, especially archaea, are adept at surviving in extreme conditions; in this case those conditions are extreme pressure, and temperatures up to 350°C (662°F)! Microbes can also be found in the freezing temperatures of the arctic. On February 6, 2013 scientists first reported bacteria found a half-mile deep under the ice of Antarctica. In fact, since the arctic isn’t hospitable to other forms of life, bacterial communities dominate the biodiversity [3].

Radiation is scary for humans even at very low doses, but there are microorganisms that can withstand extremely high levels. These microbes exhibit “radio-resistance”: resistant to ionizing radiation [4]. A lethal dose of radiation for humans is approximately 4-10 gray (Gy), while these organisms can survive radiation of at least 1000 (Gy) (100x more than humans!) The most extreme example is Thermococcus gammatolerans, rightly named after its ability to survive 30,000 (Gy)! [5]

And last, but certainly not least, there are astronaut microbes! When the unmanned lunar lander Surveyor 3 returned to earth, NASA scientists were surprised to find living Streptococcus mitis from Earth that had survived on the lander for 31 months in the vacuum of space [6].  Since then several microorganisms have been identified as having the ability to survive in space, and these include one of my favorite organisms (micro or macro): Tardigrades! Also known as “water bears”, because they literally look like little bears, these little guys are the ultimate extremophiles. Not only can they survive in space, they are also radio-resistant and can survive radiation levels up to 5,700 (Gy), as well as in temperatures below freezing and above boiling. To top it off, they can survive more than 10 years without food or water [7]. Basically, Tardigrades will outlive us all.

Some other not-so-common places that microbes are commonly found: bubbling tar, steam vents, boiling water, in soil and ice miles underground, and most likely in areas that humans have been unable to discover thus far [8].

Water Bear
 Tardigrade (Water Bear)

 

Humans and Microbes: A love-hate relationship

The term “human microbiota” is becoming increasingly well-known as we learn more about our close interactions with microorganisms, but as a short description: the human microbiota, or microflora, is the collective of microbes that live on the surface and in layers of the skin, the saliva and oral mucosa, in the conjunctiva (lines the inside of the eyelids), in the gastrointestinal tract, in the respiratory system, and in the vagina [9]. The interactions between the human body, the microbiota, and the environment are so complex that I’m not even going to go there in this post. What I do want to discuss though, is how microbes are actually helping us!

Bacteria in our body play vital roles in keeping us healthy – they interact with and boost our immune systems and even combat pathogenic microbes (ones that cause disease). The bacteria on our skin act as an extra layer of protection against any bad guys getting in or on us. In a nut-shell, having these communities of good bacteria in and on our bodies helps prevent bad communities from moving in [10]. In fact, bacteria play such an important role in our health that there are more bacterial cells in our bodies than our own actual cells [11].

Microbes are also used to improve our health and combat diseases in more targeted ways. An example of this is the use of microbes as vehicles, or carriers, for medicine. Some bacterial strains are commonly used as “delivery capsules” for drugs that are normally toxic when taken alone. E. coli has been engineered to transport an enzyme specifically to cancer cells, without targeting and harming other cells [12].

Viruses are also being used to treat cancer, as a team from Massachusetts General Hospital and Harvard Medical School used engineered Herpes Simplex Virus Type 1 (HSV-1) as vectors for targeting cancer cells [13]. Using viruses or other microbes as vehicles could eliminate more dangerous types of treatment such as chemotherapy. Microorganisms can also be genetically engineered to target tumors and specific areas of the body that are under attack from disease.

Other ways that microbes are helping us range from food production to toxic cleanup. Yeasts are commonly used for bread and beer production and various bacteria are used for cheese production. Microbes are also exploited for the compounds they make: including enzymes, vitamins, and antibiotics. For example, penicillin was originally isolated from the fungi Penicillium, and lactic acid is used as a food preservative. Microbes are also essential to agriculture and nutrient recycling. Microbes living in the soil break down nutrients that are found in their environment, and provide things like nitrogen to plants in a process called mineralization [14] (side note: bacteria also break down nutrients in the GI tract to help humans digest them better). As mentioned, microbes are also used for cleaning up environmental toxins, including oil spills. Some microorganisms actually use oil as fuel, so that they can be released into a contaminated area and, given enough time, the oil will be removed [15]. This is a promising approach to cleaning up other toxins found in soil and water in a relatively safe and hands-off way.

 

I could honestly go on and on about the wonders and curiosities of microorganisms, but for the sake of keeping at least some readers I’m going to stop here. I hope you enjoyed reading about these amazing organisms, and have a new-found or refreshed appreciation for the invisible world of microbes. Now I dare you to look at anything around you, even in the mirror, and not think about how many microorganisms are there…good luck, and welcome to my world.

 

Work Cited:

  1. http://infohost.nmt.edu/~klathrop/7characterisitcs_of_life.htm
  2. http://www.ucmp.berkeley.edu/fungi/fungi.html
  3. https://en.wikipedia.org/wiki/Archaea#Morphology
  4. http://www.microbeworld.org/types-of-microbes/bacteria/42-what-is-a-microbe-sp-828/types-of-microbes/138-bacteria
  5. https://microbewiki.kenyon.edu/index.php/Deep_sea_vent
  6. https://en.wikipedia.org/wiki/Antarctic_microorganism#Climate_and_habitat
  7.  http://morgana249.blogspot.com/2014/08/6-organisms-that-can-survive-fallout.html
  8. https://microbewiki.kenyon.edu/index.php/Thermococcus_gammatolerans
  9. http://www.panspermia.org/bacteria.htm
  10. https://en.wikipedia.org/wiki/Tardigrade
  11. http://www.livescience.com/29865-strangest-places-life-found.html
  12. https://en.wikipedia.org/wiki/Human_microbiota#Anatomical_areas
  13. http://www.scientificamerican.com/article/ultimate-social-network-bacteria-protects-health/
  14. http://schaechter.asmblog.org/schaechter/2014/07/microbial-to-human-cell-ratio-just-bragging-rights.html
  15. http://www.wpi.edu/Pubs/E-project/Available/E-project-040912-094932/unrestricted/Jared_Guttmann_Investigations_into_the_Current_Usage_of_Microbes_in_Medicine.pdf
  16. http://www.nature.com/cgt/journal/v9/n12/full/7700537a.html
  17. http://www.ext.colostate.edu/mg/gardennotes/212.html
  18. http://www.scientificamerican.com/article/how-microbes-helped-clean-bp-s-oil-spill/

Further Links: 

Wikipedia: Microorganisms  https://en.wikipedia.org/wiki/Microorganism
Fungi Information  http://www.ucmp.berkeley.edu/fungi/fungi.html
Archaea Information  https://en.wikipedia.org/wiki/Archaea#Morphology
Protista Information  http://www.microbeworld.org/types-of-microbes/protista
Virus Information  http://www.ucmp.berkeley.edu/alllife/virus.html 
Tardigrade Information  http://tardigrades.bio.unc.edu/ 


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What Do You Mean: Finding Correct Information in a World Full of Disinformation

Let’s admit it, we occasionally find ourselves quoting a study or something we saw on the internet as truth without doing much or any background research to find out if the validity holds. I’m guilty of this, and as a scientist and a writer I should probably be the first to admit it. So—what do we do about it? In other words, how do we curb our opinions and statements to better represent the truth?

I believe that everyone, no matter age or education level (let’s ignore babies for this post), has the ability to discern fact from fiction and to be a critical thinker. When it comes to being a critical thinker online, where there is a plethora of disinformation, it’s important to have some ground rules for yourself. Today I am going to share my personal ground rules, but first let’s go over certain words that are used in both common and scientific language, but that have separate meanings (e.g. theory), and how they are used to “de-bunk” science

Trust me, you have a conspiracy hypothesis.

As an English major gone Biologist, the use of the word “theory” is a source of great frustration. Theory, like many other words, has a separate meaning when used in common language versus used in scientific work.

Common use of theory: used when one has an idea or is guessing at something “my theory is…”, while often these are based on simple observations or opinion, and not on experimental data (as is done in science). I used the word conspiracy for the heading because I’m sure most people have heard of conspiracy theories. These “theories” are examples of non-scientific ideas: ones that cannot be tested repeatedly and upheld or dismissed based on experimental data. Simply, in this context, a theory is a guess.

Scientific use of theory:  “A well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method and confirmed through observation and experimentation” [1]. Took the words right out of my mouth, but in simpler terms the word theory used in scientific terms means an idea that was tested repeatedly and by multiple, independent parties and consistently upheld by the results. So, in this context, a theory is much more than a guess. A theory may be altered overtime with new supporting evidence, but it always has a strong basis of truth attached to it.

Side Note: The theory of evolution is often attacked as being “just a theory”, but it has stood the test of time and repeated experimentation. Here are some other theories that have done the same: the theory of plate tectonics, the theories of special relativity and general relativity (Einstein ring a bell?), and Heliocentrism: the theory that the Earth revolves around the sun. The beautiful thing about science, and also the thing that makes it vulnerable to nay-sayers, is that nothing can be completely proven (i.e. there must always be room for growth and change)—meaning that we, as humans, are part of this world and universe and as such, we cannot see how the it all works from the outside.

An analogy of this: you are living in a house without the blueprints. You don’t know how the house was made, but by observing and testing various components of it you come up with a theory of how it was built. As you continue to collect more information, this theory may change, but without the blueprints you will never know for certain that you are right.

So there must always be room for doubt in science, but that also means room for new knowledge and growth.

Hypothesis vs. Theory vs. Law

Briefly, I wanted to define the other terms used in science as well.

Hypothesis: you can think of a hypothesis as an educated guess (which is what most people mean when they say they have a theory). When one observes something in nature, they make a hypothesis. Example: you are walking along and notice that a moth has the same coloring as the tree it is on, so thinking about camouflage you make the following hypothesis: “the moth has the same coloring as the tree in order to hide from predators”. Now you can begin to test this hypothesis by using the scientific method. (http://www.sciencemadesimple.com/scientific_method.html)

Law: this term can be the most confusing, but I think this is a good explanation: a law is “the description of an observed phenomenon. It doesn’t explain why the phenomenon exists or what causes it” [2]. In relation to this, a theory would be the explanation of the phenomenon. Newton’s Laws of Physics are probably the most well-known laws, which describe the world around us.
(http://www.physicsclassroom.com/Physics-Tutorial/Newton-s-Laws)

How to Navigate Through the Internet

The internet can be a wonderful place for connecting to others, sharing stories, and finding useful information, but it can also be an overwhelming place full of propaganda and false information. So here are my tips for navigating to useful and correct info.

  1. Collect information from multiple sources. This is my number one tip, and even after following the next two I encourage everyone to always keep this in mind. Getting a consensus from independent sources is a way of ensuring that there is an agreement that the information is true. I usually check at least 4-5 different sources, which are not related to one another, before I feel comfortable believing the information.
  2. Avoid getting information from sources that would benefit from the info being true. This can be pretty hard, and sometimes the information is right but I would take it with a grain of salt. Some examples of this would be sites that promote ideas which backup their existence. (e.g. a site that promotes the use of a certain drug, but that site is connected to the pharmaceutical industry). The main reason to not trust the information is that it is most likely biased. The best type of info, and really the only type of information that I think anyone should want, is objective. If you are having trouble finding sites that don’t have some sort of connection to the information that is being provided, go back to tip 1 and find several independent sources.
  3.  Look for studies that include evidence supporting the information. There are studies on almost everything out there, from nutritional needs to socio-economic issues. Finding studies, especially primary literature (http://www.lib.umd.edu/tl/guides/primary-sources) can be extremely useful for figuring out a question or gaining insight into an issue since studies provide evidence that supports a conclusion, or idea, and do not simply state an opinion. 

          Here are my favorite sources for finding articles:

  1. https://scholar.google.com/ (multidisciplinary)
  2. https://doaj.org/ (multidisciplinary)
  3. http://www.jurn.org/#gsc.tab=0 (multidisciplinary)
  4. https://www.econbiz.de/ (economics)
  5. http://www.ncbi.nlm.nih.gov/pubmed (biology/medicine)
  6. http://eric.ed.gov/ (education)

So there you have it folks! The internet can be a daunting and confusing place, but with the right tools and frame of mind you can use it as a source for valuable and trustworthy information.

Final (Cheesy) Note

If we can have a society and a world that is better at critical thinking, forming opinions based on evidence, and fact-checking on their own then I think that we can promote a brighter future in all areas: environmental, educational, economic, social, etc.

And one of the major components of being a critical thinker is having the ability to admit that we are only human and that we can be mistaken or mislead, so that when new evidence presents itself we have the ability to form our opinions on what is true and not on what we want to be true.

Final, Final Note

Right before I posted this I came across this article from IFLScience and I thought it would a great piece to share since it very much falls under the same theme. The article is titled “How Misinformation Spreads on the Internet”. Enjoy! http://www.iflscience.com/technology/facebook-echo-chambers-help-spread-and-reinforce-misinformation

Thank you for reading and, as always, keep questioning! 

 

Work Cited:
  1. https://en.wikipedia.org/wiki/Scientific_theory
  2. http://www.livescience.com/21457-what-is-a-law-in-science-definition-of-scientific-law.html