Sweet Readers,
Please forgive the woeful neglect of the past weeks and months! I have been utterly swamped at work, preparing for an exciting conference and all that goes with it. I do promise to finish my GMO series very soon, as well as the epic posts that will accompany my sharing pictures of our Italian adventure with you! Look for updates within the next few weeks, once my life is a little less chaotic. In the meantime, thanks so much for your comments and inquires, and thank you for reading!!
My best,
R
Sunday, May 19, 2013
Monday, March 25, 2013
GMO or GM-No Part II
Welcome back, folks! Time for a brief round two of contentious scientific debate, R-beckers style!
We left off looking at the mechanism used in producing GMOs. You can refresh your memory here. Moving on from that, we have to ask a number of questions.
Today, though, we're only focusing on one particularly significant scientific obstacle: once we have produced this product, how to we ensure it stays consistent, generation after generation, during breeding and seed production?
To address this, we have to understand a little something about a thing called gene copy number. The copy number is exactly what it sounds like it is. It is the number of copies of one's gene of interest that are inserted in the plant (soybean for our purposes) genome during transformation. With any luck at all, our copy number will be one! However, if it isn't, (and really, it never is) we can typically breed away the extra copies we don't want. Why wouldn't we want them, you ask? Well, there are a couple of reasons:
1. Plants have a mechanism known as post-translational gene silencing. This is the mechanism by which plants prevent the expression of a particular protein product AFTER it has been translated and partially produced. This happens to genetic information native to the genome AND to information we add in the transformation process, particularly if there are multiple copies of our GOI.
2. If we are interested in using this technology to produce therapeutic proteins or as a food source, we have to ensure the expression levels of any introduced protein remains unchanged. If not, we face problems with things like "good manufacturing processes" (GMP, for you industry types) and we run the risk of alarming individuals who might be concerned with food allergens. In addition, we don't want to start out producing proteins at a gang busters level, only to diminish slowly over generations of breeding. Not a very good production model, to be sure!
So, how do we know how many copies we have? We do a technique called a Southern blot. Now, there are a couple of new-fangled ways to approach this problem that appear easier than an SB, but they are not the standard. When things change, I'll let you know! Southern blots use chemiluminescent probes (they light up xray film) to search the entire genome for a particular sequence. Using enzymes that cut up the plant genome, we fragment our DNA sample into smaller, more manageable pieces. We then run our sample out on a gel and then we use an electric current to transfer it to a probe-able membrane. We use short pieces of labeled DNA, called primers, to search for our particular sequence. Both the fragmentation pattern and the probe hybridization indicate how many copies of our sequence are present. By purposefully crossing our GMO with wild-type plants, we can, generation by generation, eliminate each genetic copy until we reach the desired single GOI.
Once we have confirmed our copy number and we know our expression level remains consistent over multiple generations, we are, as they say, cookin' with gas.
Incidentally, this process can take a number of years to accomplish. The transformation alone is difficult to achieve. There IS a reason companies like Monsanto make big bucks off this stuff...its not easy to do in a controlled and specific way!
By now you've got all the pieces for the HOW its done. Next time (heaven help me), we delve into the WHY its done; (oh good lord) WHETHER you should eat it and is it environmentally sound. Cue the hate mail (from both sides)!
See ya next time, folks!
We left off looking at the mechanism used in producing GMOs. You can refresh your memory here. Moving on from that, we have to ask a number of questions.
Today, though, we're only focusing on one particularly significant scientific obstacle: once we have produced this product, how to we ensure it stays consistent, generation after generation, during breeding and seed production?
To address this, we have to understand a little something about a thing called gene copy number. The copy number is exactly what it sounds like it is. It is the number of copies of one's gene of interest that are inserted in the plant (soybean for our purposes) genome during transformation. With any luck at all, our copy number will be one! However, if it isn't, (and really, it never is) we can typically breed away the extra copies we don't want. Why wouldn't we want them, you ask? Well, there are a couple of reasons:
1. Plants have a mechanism known as post-translational gene silencing. This is the mechanism by which plants prevent the expression of a particular protein product AFTER it has been translated and partially produced. This happens to genetic information native to the genome AND to information we add in the transformation process, particularly if there are multiple copies of our GOI.
2. If we are interested in using this technology to produce therapeutic proteins or as a food source, we have to ensure the expression levels of any introduced protein remains unchanged. If not, we face problems with things like "good manufacturing processes" (GMP, for you industry types) and we run the risk of alarming individuals who might be concerned with food allergens. In addition, we don't want to start out producing proteins at a gang busters level, only to diminish slowly over generations of breeding. Not a very good production model, to be sure!
 |
| Source: www.cytologystuff.com |
Once we have confirmed our copy number and we know our expression level remains consistent over multiple generations, we are, as they say, cookin' with gas.
Incidentally, this process can take a number of years to accomplish. The transformation alone is difficult to achieve. There IS a reason companies like Monsanto make big bucks off this stuff...its not easy to do in a controlled and specific way!
By now you've got all the pieces for the HOW its done. Next time (heaven help me), we delve into the WHY its done; (oh good lord) WHETHER you should eat it and is it environmentally sound. Cue the hate mail (from both sides)!
See ya next time, folks!
Thursday, March 14, 2013
Reflections of the once semi-devout
Yep, I used to be Catholic. For all intents and purposes, at least according to somebody's official list, I still am. Baptized as an infant; confirmed many years later....as an adult. Indeed, the choice was not thrust upon me by my parents, as is the case with so many spiritual beginnings. No, in my case, it was a very personal, intense journey that led me to the RCIA program at St. Francis of Assisi parish, in Raleigh, NC.
Up to that point, I'd dabbled in just about every possible religion in which one can dabble, with the exception of Islam and Mormonism. Certainly, my parents raised us in the Christian tradition, but it was a smattering of Catholic, a little Methodist, the occasional Episcopalian and, quite frankly, actual church attendance was rare with a few bouts of guilty medium thrown in for good measure. It was not, as they say, a priority. Given certain learning limitations of my sibling, my parents did see fit to send us to a private Baptist school for about four years, but that did more to stifle my not-so-budding faith than anything has since.
My personal investigation into this thing we call God started in earnest mid-way through college. Washed out of the USCGA and in rehab for knee injuries, I could no longer do the things I loved, so I followed a friend to a Christian sorority. Let's say that was the biggest disaster known to man and leave it at that. Honestly, it was more the sorority bit and notsomuch the Christian bit that drove me nuts. Around that same time, I made friends with a number of local pagans/wiccans/free spirits and was drawn into THAT circle. It stuck for awhile, and I remain friends with some of the most amazing men and women I've met to date. Their kindness and generosity was a testament to their beliefs...but its hard for a scientist to suspend reality and the laws of physics that much.
Finally, in the fall of my junior year, a dormitory friend dragged me to mass. It was beautiful. I was so enamored by the whole thing and the pull was so strong that I immediately sought out an RCIA program for adult confirmation. It took a few false starts, but then I discovered St. Francis. Being hippy-ish at the time, it should surprise no one that I was drawn to a parish in the Franciscan tradition. Simple, down-to-earth celebrations of beauty and goodness....count me in! I absolutely adored my RCIA group, my leaders and the Friars who guided us. I STILL adore the vast majority of those people, and they remain examples of who I want to be when I finally get my shit together.
As things evolved, I began to explore the idea of religious life. I talked with one of the Friars at St. Francis, and he suggested a number of orders to check out. I followed up on three of them, one of which necessitated a change of flight time rescue and a rehabilitation night out (I still owe you for that, Jules!). One, however, caught my attention and I took it so far as to work with the vocation director (still a dear friend) and start the process of joining the community.
By the time I graduated from NCSU, I'd changed my graduate school plans and was headed for a master's degree program at Washington Theological Union, complete with an scholarship from the Friars of OFM.
I lasted six weeks.
You can take the girl out of the lab, apparently....but she won't like it and will need to go back as soon as humanly possible. So, I did. I came home to Charlotte and started the program at UNCC, the rest of my academic career being history. It was during that time I realized the idea of running away from pain was driving a number of my decisions and I should probably back off and get my head screwed on straight. So, I took a deep breath and decided in lieu of community life, I would go for a PhD. At this point, the conversation was a difficult one, as I had close friends in this community, but they never wavered in their support of my journey and their understanding of my need to "go it alone".
I searched the Charlotte area long and hard for a parish to call home. I spent weeks exploring each option, methodically and slowly, believing I would find a community just as welcoming and beautiful as the one in Raleigh I so deeply loved. To make a long story short, that didn't happen. Not. Even. Close. The diocese of Charlotte is drastically different, and its bishop (whose name is Jugis...three guesses what I call him!!) is.....interesting. It was here I first experienced the "second class citizenship" many refer to when discussing the role of women in the Catholic church. Here's lookin' at YOU, St. John Neumann!
The more I struggled with finding a parish home, as opposed to a place to simply fulfill my Eucharistic obligation, the more I started to sit back and ask the big questions. Did I really believe this stuff? Can I really be affiliated with an organization that let its leaders behave this way? Was it worth it? The answer, as it turned out, was absolutely, unequivocally...no. This religion, these beliefs...they just didn't jive with the world as I saw it (from a very scientific pair of spectacles), and what I was hearing about how women should behave and what constituted sin or wrongdoing was in direct conflict with what I know, at the core of my being, to be true. I realized it wasn't the Catholic faith I'd fallen in love with; it wasn't the idea of a savior or even the person of Jesus (who, by the way, is fascinating and mysterious). What was so dear to me was the people I'd found at St. Francis and as a result of the religious community I'd explored...those beautiful people with their incredible kindness, openness to all and zest for life. Certainly, they will say their faith informs those things, and I believe them! I just know that all persons of faith are not that way. For me, though, it is the people I love, not the God.
Honestly, calling myself a Catholic or a Christian now would, in my mind, be insulting to those for whom those labels carry intense meaning, so I stopped. I read Hitchens and Dawkins with a slightly different eye now, and while I think the approach is a little wanting and a tad harsh (okay, downright mean sometimes), some of the points are valid. However, the spirit of someone like St. Francis or Claire...or Deb or Jules or Bill.... is one to which I still aspire. I might not be moved by the holy spirit, but I do hope I foster love, kindness and tolerance in my life and offer these things to those with whom I interact.
So there you have it...that's the evolution (in brief) that led me to my current place. There have been questions, and not just a little bit of concern. If this doesn't alleviate the concern, at least it'll answer the questions.
Peace and all good, friends.
Up to that point, I'd dabbled in just about every possible religion in which one can dabble, with the exception of Islam and Mormonism. Certainly, my parents raised us in the Christian tradition, but it was a smattering of Catholic, a little Methodist, the occasional Episcopalian and, quite frankly, actual church attendance was rare with a few bouts of guilty medium thrown in for good measure. It was not, as they say, a priority. Given certain learning limitations of my sibling, my parents did see fit to send us to a private Baptist school for about four years, but that did more to stifle my not-so-budding faith than anything has since.
My personal investigation into this thing we call God started in earnest mid-way through college. Washed out of the USCGA and in rehab for knee injuries, I could no longer do the things I loved, so I followed a friend to a Christian sorority. Let's say that was the biggest disaster known to man and leave it at that. Honestly, it was more the sorority bit and notsomuch the Christian bit that drove me nuts. Around that same time, I made friends with a number of local pagans/wiccans/free spirits and was drawn into THAT circle. It stuck for awhile, and I remain friends with some of the most amazing men and women I've met to date. Their kindness and generosity was a testament to their beliefs...but its hard for a scientist to suspend reality and the laws of physics that much.
 |
| Franciscan Tau |
As things evolved, I began to explore the idea of religious life. I talked with one of the Friars at St. Francis, and he suggested a number of orders to check out. I followed up on three of them, one of which necessitated a change of flight time rescue and a rehabilitation night out (I still owe you for that, Jules!). One, however, caught my attention and I took it so far as to work with the vocation director (still a dear friend) and start the process of joining the community.
By the time I graduated from NCSU, I'd changed my graduate school plans and was headed for a master's degree program at Washington Theological Union, complete with an scholarship from the Friars of OFM.
I lasted six weeks.
You can take the girl out of the lab, apparently....but she won't like it and will need to go back as soon as humanly possible. So, I did. I came home to Charlotte and started the program at UNCC, the rest of my academic career being history. It was during that time I realized the idea of running away from pain was driving a number of my decisions and I should probably back off and get my head screwed on straight. So, I took a deep breath and decided in lieu of community life, I would go for a PhD. At this point, the conversation was a difficult one, as I had close friends in this community, but they never wavered in their support of my journey and their understanding of my need to "go it alone".
I searched the Charlotte area long and hard for a parish to call home. I spent weeks exploring each option, methodically and slowly, believing I would find a community just as welcoming and beautiful as the one in Raleigh I so deeply loved. To make a long story short, that didn't happen. Not. Even. Close. The diocese of Charlotte is drastically different, and its bishop (whose name is Jugis...three guesses what I call him!!) is.....interesting. It was here I first experienced the "second class citizenship" many refer to when discussing the role of women in the Catholic church. Here's lookin' at YOU, St. John Neumann!
The more I struggled with finding a parish home, as opposed to a place to simply fulfill my Eucharistic obligation, the more I started to sit back and ask the big questions. Did I really believe this stuff? Can I really be affiliated with an organization that let its leaders behave this way? Was it worth it? The answer, as it turned out, was absolutely, unequivocally...no. This religion, these beliefs...they just didn't jive with the world as I saw it (from a very scientific pair of spectacles), and what I was hearing about how women should behave and what constituted sin or wrongdoing was in direct conflict with what I know, at the core of my being, to be true. I realized it wasn't the Catholic faith I'd fallen in love with; it wasn't the idea of a savior or even the person of Jesus (who, by the way, is fascinating and mysterious). What was so dear to me was the people I'd found at St. Francis and as a result of the religious community I'd explored...those beautiful people with their incredible kindness, openness to all and zest for life. Certainly, they will say their faith informs those things, and I believe them! I just know that all persons of faith are not that way. For me, though, it is the people I love, not the God.Honestly, calling myself a Catholic or a Christian now would, in my mind, be insulting to those for whom those labels carry intense meaning, so I stopped. I read Hitchens and Dawkins with a slightly different eye now, and while I think the approach is a little wanting and a tad harsh (okay, downright mean sometimes), some of the points are valid. However, the spirit of someone like St. Francis or Claire...or Deb or Jules or Bill.... is one to which I still aspire. I might not be moved by the holy spirit, but I do hope I foster love, kindness and tolerance in my life and offer these things to those with whom I interact.
So there you have it...that's the evolution (in brief) that led me to my current place. There have been questions, and not just a little bit of concern. If this doesn't alleviate the concern, at least it'll answer the questions.
Peace and all good, friends.
Friday, March 08, 2013
Fear of Flying
As a type A personality, I am loathe to admit when I am either not good at something or afraid of something. Through the vast majority of the last 30 years, I can count on one hand the times I remember being afraid:
1. My first time on a horse (6 or 7 years old)
2. My first time jumping off a raft into lake water (I think I was 5)
3. Standing on the platform at USCGA facing a required 15 meter fall (Sadly, 19)
4. The day I defended my dissertation (too old to confess)
5. The day I interviewed for my first post-doctoral position (ditto)
If you will notice, 3 of the 5 instances that stand out in my memory as true, paralyzing fear have to do with physical harm. In other words, I am appropriately and evolutionarily programmed to dislike things that might kill me. There is not a thing in the world wrong with a healthy fear of falling. People who tremble at heights do not do so because they are high off the ground. They do so because the ground could, at any moment, rush up to meet them and cut life short rather abruptly. Quite frankly, you crazy people who defy gravity without a second's thought are not evolutionarily advantageous to the propagation of our species! Honestly, I'm okay with this particular fear of mine. I push myself on a regular basis to overcome it in gentle ways: rock climbing, flying, careening along winding roads that hang in mid-Italian air, yoga inversions, etc, etc. I'm quite comfortable with where I've landed on this spectrum. I'm not paralyzed by my fear, but I have a healthy understanding of it and, at times, appreciation for it.
No, my well-documented fear of heights and physical falling doesn't bother me. What bothers me is something entirely new that has recently presented itself, newly minted as a challenge for my 30th year of existence. I have noticed, in recent months, that fear in general has integrated itself into my day-to-day life. Suddenly, I find it difficult to engage in challenging work conversations and defend my data. I wake up at 2am panicking from nightmares of being abandoned by loved ones. I dwell more frequently than I ought on the possibility of failing in my chosen profession and becoming a poverty statistic, and, most obviously, I have become completely incapable of even attempting a middle-of-the-room handstand; something I willingly failed at a gazillion times before without injury and a fear that does not extend to inversions I've already mastered.
If you look closely, there is a common thread through all of these things. If you've already spotted it, then you are much quicker on the uptake than I was. In fact, it took a whole other perspective, in the form of my beautiful ashtanga yoga teacher, for me to realize what exactly was going on. After explaining my new found fear of handstands, she quietly mused...."Could it be a fear of failing, maybe?"
Could it??!!! HA! Of course it could...of course it is! I am firmly in the clutches of a mid-life panic attack, spurred on by the idea that there is no safety net and, if I fail, there will be no recovery.
The problem with such a state of mind is that, so far, it gels around the idea of failure. I weigh risks very differently in this mind-set and waste precious time coaxing myself off the wall to face my demons, often without much progress. I am less able to envision success and generate ideas for the future. In being afraid of falling, I have also become afraid to fly.
The good thing about all of this is that it would seem I am very aware of what's happening. This is by no means a subconscious issue. I grapple with it daily. Certainly, the reasons for it may lie deep within the confines of my long-term memory archives, but nonetheless, the issue is front and center. I recently came across a wonderful video by my other lovely ashtanga teacher, Kino Macgregor, about how to fall when practicing handstand. I think the analogy is fairly clear, and I play the video back to myself almost every day. For now, I grapple with learning how to fail and how getting back up again might look. There's no happy ending fable to this one, at least not right now. This is life, in real time...and I'm still learning how to live it!
1. My first time on a horse (6 or 7 years old)
2. My first time jumping off a raft into lake water (I think I was 5)
3. Standing on the platform at USCGA facing a required 15 meter fall (Sadly, 19)
4. The day I defended my dissertation (too old to confess)
5. The day I interviewed for my first post-doctoral position (ditto)
If you will notice, 3 of the 5 instances that stand out in my memory as true, paralyzing fear have to do with physical harm. In other words, I am appropriately and evolutionarily programmed to dislike things that might kill me. There is not a thing in the world wrong with a healthy fear of falling. People who tremble at heights do not do so because they are high off the ground. They do so because the ground could, at any moment, rush up to meet them and cut life short rather abruptly. Quite frankly, you crazy people who defy gravity without a second's thought are not evolutionarily advantageous to the propagation of our species! Honestly, I'm okay with this particular fear of mine. I push myself on a regular basis to overcome it in gentle ways: rock climbing, flying, careening along winding roads that hang in mid-Italian air, yoga inversions, etc, etc. I'm quite comfortable with where I've landed on this spectrum. I'm not paralyzed by my fear, but I have a healthy understanding of it and, at times, appreciation for it.
No, my well-documented fear of heights and physical falling doesn't bother me. What bothers me is something entirely new that has recently presented itself, newly minted as a challenge for my 30th year of existence. I have noticed, in recent months, that fear in general has integrated itself into my day-to-day life. Suddenly, I find it difficult to engage in challenging work conversations and defend my data. I wake up at 2am panicking from nightmares of being abandoned by loved ones. I dwell more frequently than I ought on the possibility of failing in my chosen profession and becoming a poverty statistic, and, most obviously, I have become completely incapable of even attempting a middle-of-the-room handstand; something I willingly failed at a gazillion times before without injury and a fear that does not extend to inversions I've already mastered.
If you look closely, there is a common thread through all of these things. If you've already spotted it, then you are much quicker on the uptake than I was. In fact, it took a whole other perspective, in the form of my beautiful ashtanga yoga teacher, for me to realize what exactly was going on. After explaining my new found fear of handstands, she quietly mused...."Could it be a fear of failing, maybe?"
Could it??!!! HA! Of course it could...of course it is! I am firmly in the clutches of a mid-life panic attack, spurred on by the idea that there is no safety net and, if I fail, there will be no recovery.
The problem with such a state of mind is that, so far, it gels around the idea of failure. I weigh risks very differently in this mind-set and waste precious time coaxing myself off the wall to face my demons, often without much progress. I am less able to envision success and generate ideas for the future. In being afraid of falling, I have also become afraid to fly.
The good thing about all of this is that it would seem I am very aware of what's happening. This is by no means a subconscious issue. I grapple with it daily. Certainly, the reasons for it may lie deep within the confines of my long-term memory archives, but nonetheless, the issue is front and center. I recently came across a wonderful video by my other lovely ashtanga teacher, Kino Macgregor, about how to fall when practicing handstand. I think the analogy is fairly clear, and I play the video back to myself almost every day. For now, I grapple with learning how to fail and how getting back up again might look. There's no happy ending fable to this one, at least not right now. This is life, in real time...and I'm still learning how to live it!
P.S. Yes, I absolutely stole my title from the incomparable Erica Jong.
Friday, February 22, 2013
GMO or GM-No...Part I
Here it goes...this is me, diving headfirst into the MOST contentious scientific debate I know (with the exception of evolution v. intelligent design, but really, unless you're mildly "touched" as my Dad would say, that's not a debate worth having).
Let's start somewhat small and digest this monster in manageable bites.
First, what exactly does GMO really mean?
GMO is short-hand for "genetically modified organism". This includes any bacterium, fungus, virus, plant or animal whose genetic composition (its DNA) has been permanently altered. Routine examples of this (that you don't really think about) are often found in vaccine development, including the nasal form of the flu vaccine (which is a live virus that has been modified to remove its pathogenicity or disease-inflicting ability), the polio vaccine and countless others.
Most of these examples deal with viruses. Bacteria and viruses have a fairly simplistic DNA genome (complete set of all the genes in a given organism) and are, thus, fairly easy to manipulate. In nature, bacteria acquire genes and offer up some of their own through a process called horizontal gene transfer, where the basic level of genetic information, DNA, is physically "traded" from one bacterium to another. This explains why some forms of, for example, E. coli, are harmful while others are not. The harmless strains have no acquired the necessary genes or genetic modifications to be dangerous. Additionally, any ninth grader in freshman biology can offer up a basic explanation of mutation.
Our bodies have rigorous machinery by which our DNA is replicated and turned into protein for functionality (transcription and translation ought to jog a long-lost high school memory). All other organisms have similar machinery to some degree or other. Bacteria and viruses have the simplest, while mammals, reptiles and such have the most complicated. Regardless, this machinery does a bang up job, most of the time. It does, on occasion, make mistakes though. 99.9% of the time, those mistakes are snuffed out by the cellular machinery, or, if they aren't detected, they are harmless. This is particular true with higher order organisms. The lower order guys are much, much more prone to integrating those mutations and, the accumulation of them over time, leads to a heightened rate of evolution in those particular species.
Still with me? For right now, this is all background information! It's important because the development of higher order GMOs comes from the use of processes that already exist in nature; its just about our ability to manipulate them! Keep in mind we are not anywhere close to addressing the good v. bad or right v. wrong question yet! We have to understand before we make judgments!
Okay, let's keep truckin'....
Now that we know what GMO means and we know that a form of genetic sharing occurs in nature without any input from us, we can begin to talk about how GMO technology is used. In Part II, we'll take a look at genetically modified animals, but for today, let's stick to plants. GMO crops are hugely contentious, much more so than animals, because, predominantly, the technology is being implemented in most of our daily lives.
When a company, lab group or scientist wants to take a gene from one organism and put it in another, the best means of doing so is via horizontal gene transfer. That's right!! It's the same process bacteria use to share their DNA! Every gene in every organism is made up of some sequence of four basic components, known as nucleotides (A,T,C,G anyone???). Using that specific sequence, scientists can replicate their gene of interest (GOI) outside of the organism from which it came. To do this, we isolate the genetic material from the organism in question and we use a process called Polymerase Chain Reaction (PCR) to amplify the particular region in which we have interest. Dr. Kary Mullis received the Nobel Prize in 1993 for developing this technology and jump-started the biotechnology revolution of the 1990's. Once we have our GOI, we coax bacteria to take up our DNA and retain it. You will often see reference to "competent" bacteria, which simply means the membranes of said bacteria are permeable to the uptake of DNA pieces.
Remember, this happens ALL the time in nature. We've just managed a way of mimicking it in the lab environment with a lot more specificity and a lot less risk.
Update: The previous statement has caused some ire in my personal scientific community, so allow me to clarify. No, an artificial plasmid with a particular GOI does NOT find its way into plants from bacteria unaided by human intervention. When I say this "happens ALL the time", I am referring to the process of transferring some non-specific DNA from Agro to the infected plant, with no benefit to the plant. The process is what we've hijacked for our purposes. In addition, there are documented cases of cell to cell signaling/communication where a prokaryote (i.e. bacterium) transfers information to a eukaryote (i.e. plant), but that is still an as yet not well understood process that isn't really relevant to this particular discussion.
Once our bacteria, usually a species known as Agrobacterium tumefaciens, has taken up our GOI, we let nature do the rest. Agro, as it is often known in scientific circles, causes a disease in plants, known as crown-gall disease. Typically found at the roots, Agro causes tumors to grow on plants and hijacks the plant cellular machinery for its own purposes. In so doing, genetic material is traded from bacterium to plant.
So, in the lab, we cause a mild injury to a small piece of tissue from our plant of interest (typically corn, soybean, wheat, etc) and we "infect" the wound with the Agro that carries our GOI. This is done in an otherwise sterile environment, under a tissue culture hood. This ensures only our Agro infects the plants and there is no fungal contamination. This piece of tissue is cultured in the same way a seed would be, with the necessary hormones and growth factors being added to the media in which it grows. Once the plant is fully grown, it is moved to a normal soil environment. Our "parent plant", as we call it, then produces seeds. The vast majority of those seeds will NOT contain our GOI, but, if we do it right, a small percentage will! Those seeds can then be grown up to produce genetically modified crops or become a source for a particular purified protein.
So there you have it! This is what I might call the 'bare bones basics' of how GMOs are generated. Take a bit of time to wrap your mind around it if its new, and please feel free to ask questions in the comments! In the next round, we'll take a look at gene copy number and how to ensure GM crops are the same generation after generation!
Stay tuned!
Just a friendly reminder: we play nice here! All respectful and kind comments or questions are welcome and appreciated. Remember what your Mama told you, if you can't say something nice.....
Let's start somewhat small and digest this monster in manageable bites.
First, what exactly does GMO really mean?
GMO is short-hand for "genetically modified organism". This includes any bacterium, fungus, virus, plant or animal whose genetic composition (its DNA) has been permanently altered. Routine examples of this (that you don't really think about) are often found in vaccine development, including the nasal form of the flu vaccine (which is a live virus that has been modified to remove its pathogenicity or disease-inflicting ability), the polio vaccine and countless others.
Most of these examples deal with viruses. Bacteria and viruses have a fairly simplistic DNA genome (complete set of all the genes in a given organism) and are, thus, fairly easy to manipulate. In nature, bacteria acquire genes and offer up some of their own through a process called horizontal gene transfer, where the basic level of genetic information, DNA, is physically "traded" from one bacterium to another. This explains why some forms of, for example, E. coli, are harmful while others are not. The harmless strains have no acquired the necessary genes or genetic modifications to be dangerous. Additionally, any ninth grader in freshman biology can offer up a basic explanation of mutation.
Our bodies have rigorous machinery by which our DNA is replicated and turned into protein for functionality (transcription and translation ought to jog a long-lost high school memory). All other organisms have similar machinery to some degree or other. Bacteria and viruses have the simplest, while mammals, reptiles and such have the most complicated. Regardless, this machinery does a bang up job, most of the time. It does, on occasion, make mistakes though. 99.9% of the time, those mistakes are snuffed out by the cellular machinery, or, if they aren't detected, they are harmless. This is particular true with higher order organisms. The lower order guys are much, much more prone to integrating those mutations and, the accumulation of them over time, leads to a heightened rate of evolution in those particular species.
Still with me? For right now, this is all background information! It's important because the development of higher order GMOs comes from the use of processes that already exist in nature; its just about our ability to manipulate them! Keep in mind we are not anywhere close to addressing the good v. bad or right v. wrong question yet! We have to understand before we make judgments!
Okay, let's keep truckin'....
Now that we know what GMO means and we know that a form of genetic sharing occurs in nature without any input from us, we can begin to talk about how GMO technology is used. In Part II, we'll take a look at genetically modified animals, but for today, let's stick to plants. GMO crops are hugely contentious, much more so than animals, because, predominantly, the technology is being implemented in most of our daily lives.
When a company, lab group or scientist wants to take a gene from one organism and put it in another, the best means of doing so is via horizontal gene transfer. That's right!! It's the same process bacteria use to share their DNA! Every gene in every organism is made up of some sequence of four basic components, known as nucleotides (A,T,C,G anyone???). Using that specific sequence, scientists can replicate their gene of interest (GOI) outside of the organism from which it came. To do this, we isolate the genetic material from the organism in question and we use a process called Polymerase Chain Reaction (PCR) to amplify the particular region in which we have interest. Dr. Kary Mullis received the Nobel Prize in 1993 for developing this technology and jump-started the biotechnology revolution of the 1990's. Once we have our GOI, we coax bacteria to take up our DNA and retain it. You will often see reference to "competent" bacteria, which simply means the membranes of said bacteria are permeable to the uptake of DNA pieces.
Remember, this happens ALL the time in nature. We've just managed a way of mimicking it in the lab environment with a lot more specificity and a lot less risk.
Update: The previous statement has caused some ire in my personal scientific community, so allow me to clarify. No, an artificial plasmid with a particular GOI does NOT find its way into plants from bacteria unaided by human intervention. When I say this "happens ALL the time", I am referring to the process of transferring some non-specific DNA from Agro to the infected plant, with no benefit to the plant. The process is what we've hijacked for our purposes. In addition, there are documented cases of cell to cell signaling/communication where a prokaryote (i.e. bacterium) transfers information to a eukaryote (i.e. plant), but that is still an as yet not well understood process that isn't really relevant to this particular discussion.
Once our bacteria, usually a species known as Agrobacterium tumefaciens, has taken up our GOI, we let nature do the rest. Agro, as it is often known in scientific circles, causes a disease in plants, known as crown-gall disease. Typically found at the roots, Agro causes tumors to grow on plants and hijacks the plant cellular machinery for its own purposes. In so doing, genetic material is traded from bacterium to plant.
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| Source: www.bio.davidson.edu |
So there you have it! This is what I might call the 'bare bones basics' of how GMOs are generated. Take a bit of time to wrap your mind around it if its new, and please feel free to ask questions in the comments! In the next round, we'll take a look at gene copy number and how to ensure GM crops are the same generation after generation!
Stay tuned!
Just a friendly reminder: we play nice here! All respectful and kind comments or questions are welcome and appreciated. Remember what your Mama told you, if you can't say something nice.....
Wednesday, February 20, 2013
I am you and you are me and we are all together...
Hello blog friends!! I know, I know. Most of you are hoping for ten installments of every Italian detail I can muster....and you'll get it! I promise....just not today.
Today I've got some musings for you to ponder, because when I can't work something out in my head, I come here, to my keyboard and the quiet, and I see what the words tell me. Incidentally, I know a good many of you disagree with my interpretation, but I appreciate your audience and your willingness to hold space for the ideas anyway.
So, to the words....
An old demon came roaring back today. I discovered, in my company's yearly "healthy weight" weigh-in that I am, in fact, 1.5 inches shorter than I thought. Seriously, Rebecca? That's a demon?! Well, no, it isn't. However, what that meant for me was that I was not in the category I thought I was for healthy weight range. Being shorter, you guessed it, means you have to weigh less. As it turned out, I still fell within the healthy range, but by a much smaller margin than I initially anticipated. While the nurse recording my numbers was very kind, as my disappointment was etched all over my face, her well-intentioned "it's alright dear, you're in range and that's what counts" did little to assuage my anxiety. Without getting into the numbers, because I'm certain THAT would give me a stroke on the spot, let's just say I have waged the body image battle in every possible way for the vast majority of my life. Since the universe saw fit, in the last few years, to bless me with genetic malfunctions that actually make that battle even harder, I'm more than willing to admit I'm extraordinarily oversensitive about it.
I left the clinic office disgruntled, to say the very least. Oddly enough, my issues followed me out the door! Funny how they're sneaky that way, isn't it?! They cropped up again and again throughout the afternoon and evening, mostly in the form of "friendly" commentary and a few well-placed zingers designed to highlight my insecurities. To be frank, this whole fiasco started last week with a couple of isolated incidents that didn't give me much pause, but planted themselves quietly in the back of my mind and waited for their fertilizer. They got it today and, my oh my, how quickly they grew!
By the time I brought my very grumpy self home from work, I was in knots over imagined weight gain and all the horrors it would wreck upon my life. Then, I did what all women do when they can't untangle their own minds....I got on the line with my favorite one! She talked me down from the cliff of three hour cardio marathons and 25 day juice cleanses. She reminded me that my mad yoga skills do not come from being small and weak, but from building muscle and strength in a way that, sure, adds weight but gives definition and health!
When I could breathe again (thank you, SF!!!), I did do a workout...a normal one, quite honestly a somewhat easy one. Then I realized it was time to sit.
So here I am, sitting, thinking, writing, asking....
How would it be if we took the time to think about how things sound before we say them? Certainly, there are a myriad of things we should express our opinions about and get into arguments over. However, when we deal with those we call friends and lovers, should we not take a gentler approach? I'll confess, this is really hard for me. Speaking my mind is something I've been trained to do. I know, though, the times where I've paused, kept a thought or two to myself, bit my tongue when I was dying to have my say...those are the times when the outcome has been better, kinder, more loving, more useful.
Even more than that, how would it be if I was able to withhold a strong response when someone doesn't take the time to consider their words? What happens when an unkind comment or a "joke" about a sensitive topic wings my way? What if I'm not in the mood to laugh it off and join the fun? (If I were, I probably wouldn't take issue with it in the first place!) How do I turn inward and slow the flow of words, bite back the retort that comes from a place of pain and offer instead a compassionate, loving response? If that's just not possible, how do I remain silent? Every single instance in which I have responded to pain and hurt with pain, hurt and insecurity (which, by the by, looks an awful lot like sarcasm most of the time), the situation has only escalated and caused more internal chaos. I then feel badly about the other person and my response to that individual. Way to double the load! So, because I don't really have the answers, I offer this:
Pause. Stop for a millisecond and consider the person you face is a part of you. You are made of the same stardust from the far reaches of the universe. You share carbon and nitrogen recycled through the ages from the time of the dinosaurs. You are, literally, connected. Think about how your words would sound in your own ears and speak from THAT place. If you do it, and I do it, and we remind each other to do it, well then...we're really onto something, aren't we?
Today I've got some musings for you to ponder, because when I can't work something out in my head, I come here, to my keyboard and the quiet, and I see what the words tell me. Incidentally, I know a good many of you disagree with my interpretation, but I appreciate your audience and your willingness to hold space for the ideas anyway.
So, to the words....
An old demon came roaring back today. I discovered, in my company's yearly "healthy weight" weigh-in that I am, in fact, 1.5 inches shorter than I thought. Seriously, Rebecca? That's a demon?! Well, no, it isn't. However, what that meant for me was that I was not in the category I thought I was for healthy weight range. Being shorter, you guessed it, means you have to weigh less. As it turned out, I still fell within the healthy range, but by a much smaller margin than I initially anticipated. While the nurse recording my numbers was very kind, as my disappointment was etched all over my face, her well-intentioned "it's alright dear, you're in range and that's what counts" did little to assuage my anxiety. Without getting into the numbers, because I'm certain THAT would give me a stroke on the spot, let's just say I have waged the body image battle in every possible way for the vast majority of my life. Since the universe saw fit, in the last few years, to bless me with genetic malfunctions that actually make that battle even harder, I'm more than willing to admit I'm extraordinarily oversensitive about it.
I left the clinic office disgruntled, to say the very least. Oddly enough, my issues followed me out the door! Funny how they're sneaky that way, isn't it?! They cropped up again and again throughout the afternoon and evening, mostly in the form of "friendly" commentary and a few well-placed zingers designed to highlight my insecurities. To be frank, this whole fiasco started last week with a couple of isolated incidents that didn't give me much pause, but planted themselves quietly in the back of my mind and waited for their fertilizer. They got it today and, my oh my, how quickly they grew!
By the time I brought my very grumpy self home from work, I was in knots over imagined weight gain and all the horrors it would wreck upon my life. Then, I did what all women do when they can't untangle their own minds....I got on the line with my favorite one! She talked me down from the cliff of three hour cardio marathons and 25 day juice cleanses. She reminded me that my mad yoga skills do not come from being small and weak, but from building muscle and strength in a way that, sure, adds weight but gives definition and health!
When I could breathe again (thank you, SF!!!), I did do a workout...a normal one, quite honestly a somewhat easy one. Then I realized it was time to sit.
So here I am, sitting, thinking, writing, asking....
How would it be if we took the time to think about how things sound before we say them? Certainly, there are a myriad of things we should express our opinions about and get into arguments over. However, when we deal with those we call friends and lovers, should we not take a gentler approach? I'll confess, this is really hard for me. Speaking my mind is something I've been trained to do. I know, though, the times where I've paused, kept a thought or two to myself, bit my tongue when I was dying to have my say...those are the times when the outcome has been better, kinder, more loving, more useful.
Even more than that, how would it be if I was able to withhold a strong response when someone doesn't take the time to consider their words? What happens when an unkind comment or a "joke" about a sensitive topic wings my way? What if I'm not in the mood to laugh it off and join the fun? (If I were, I probably wouldn't take issue with it in the first place!) How do I turn inward and slow the flow of words, bite back the retort that comes from a place of pain and offer instead a compassionate, loving response? If that's just not possible, how do I remain silent? Every single instance in which I have responded to pain and hurt with pain, hurt and insecurity (which, by the by, looks an awful lot like sarcasm most of the time), the situation has only escalated and caused more internal chaos. I then feel badly about the other person and my response to that individual. Way to double the load! So, because I don't really have the answers, I offer this:
Pause. Stop for a millisecond and consider the person you face is a part of you. You are made of the same stardust from the far reaches of the universe. You share carbon and nitrogen recycled through the ages from the time of the dinosaurs. You are, literally, connected. Think about how your words would sound in your own ears and speak from THAT place. If you do it, and I do it, and we remind each other to do it, well then...we're really onto something, aren't we?
Monday, December 17, 2012
Anger and heartbreak....
I should probably start this one with yet another disclaimer. I am angry. I am furious. I am heartbroken. This is my place to be all of those things in print, say what's on my mind and feel how I want and need to feel. That being said, I'm about to say a few things that more than a few people aren't going to like. Given the atrocities of the last week and some of the responses to it, I don't really care.
Twenty beautiful children, six astoundingly brave adults and two tortured individuals are dead. They are not in heaven with the angels. They are not watching over their parents, siblings and friends with tender looks on their faces, waiting for the day that those people will join them in paradise. Nor are they burning for their acts of madness or lack thereof. They are dead. Gone. Snuffed out. A 20-year-old gunman ended any chance any of those children or young adults had at a life lived long and plentiful, because this life is the only chance we get. I do not dare give myself the false comfort of an afterlife for these innocents , because that somehow lessens the impact of what has happened to them. I hear how they are in "a better place" now. Indeed, they no longer suffer, but no, it is not a better place. They have ceased to exist, no more than stardust in the memory of the universe. The finality of that gives me pause in a way "playing with the angels" and being "with their Savior" does not. It generates a much more urgent need (in me, at least) to address the issues that brought about this act of senseless violence and rage.
There are those who would say our failure to allow prayer in schools is to blame and some deity (insert your choice here) is bringing judgment on our country. I even saw a post about how a small child said the Christian God would protect her private school because they prayed every morning. For those of you to whom the logical failings of this are NOT obvious, I offer this: Any suggestion that an omniscient, omnipotent, all loving "God" would answer the prayers of one set of children over the cries for help of another set is complete bollocks. That would require a rather great number of exceptions to the laws of physics and general relativity, not to mention the biological pathways that would require rerouting in "real time" to ensure the perpetrator of mass murder shoots the right kids. It sounds ridiculous because it is. No god caused this problem, and I can assure you, no god will solve it.
I do not believe that better gun control is the answer. I do not think the failure to properly parent is the explanation. I do not think any response that lays blame on an arbitrary organization like the NRA is appropriate. It will not be until we, as a society, are willing to step up and take collective blame for our failure to ACT that we will see change. We must accept our own failings and work to alter our current reality.
As it stands, there are few doctors/psychologists/psychiatrists who stand ready to acknowledge that a child can be anything but good, decent and innocent. Countless parents (and I know some of them) struggle with the idea that their child is different, not quite right, even dangerous and exhaust all resources, both financial and emotional, trying to find some way, any way to get their children help. Society blames these people for not being better parents, for not putting their guns away, for not paying enough attention, for not knowing what the hell to do! These children are given every excuse in the world: they MUST be victims of abuse, they MUST have suffered some trauma, they MUST NOT be to blame. Right up until they turn 18, and all hope of actually helping them is lost forever, they are shunted from group to group, doctor to doctor, with no one willing to say that they are simply not normal and should remain under constant care and observation. No, these disturbed individuals are not to blame for their conditions. There is an underlying neuropathology that science simply does not yet have the tools to understand. It is no one's FAULT that these people are the way they are. It is OUR FAULT that we choose to ignore the reality that is before us. So I will say it now: not everyone deserves a chance at a "normal" life. Not everyone should be allowed to mingle with society. Sometimes it is in the best interest of an individual AND society for that person to be removed and cared for in a remote place, in such a way as to ensure their safety and the safety of others. Life, liberty and individual freedom for all is simply not possible sometimes, and the sooner we embrace that notion, the better off we're going to be.
Once we come to terms with the idea that some people are really and truly, at their core, not okay, then we can start to take steps to ensure those people get the help they need to live as close to a normal life as can be considered SAFE for the rest of us. We cannot address the problem until we acknowledge it exists. We cannot develop the programs and do the research that will help us explain the pathology of what happens to these individuals until we recognize that something IS happening to them and it isn't typical.
Doing the work I do, I am literally surrounded by the most brilliant minds on earth. The scientific community is a small one, and we all hit a basal level of intelligence. The truly intelligent, stand-out minds are easy to identify, because they aren't like the rest of us. They think differently; they work differently; they function in a way that is entirely other from the rest of our community. I would venture that most scientists and engineers function in a slightly different way from, say, folks in the humanities, but when there's a stand-out from the stand-outs, somebody better start paying attention.
These shootings are not the fault of parents, juvenile courts, the educational system or gun enthusiasts...they are the fault of all of us, for refusing to acknowledge the truth, in the hopes that we wouldn't have to pay the price. Well, news flash, the bill just came due and there are no refunds.
Twenty beautiful children, six astoundingly brave adults and two tortured individuals are dead. They are not in heaven with the angels. They are not watching over their parents, siblings and friends with tender looks on their faces, waiting for the day that those people will join them in paradise. Nor are they burning for their acts of madness or lack thereof. They are dead. Gone. Snuffed out. A 20-year-old gunman ended any chance any of those children or young adults had at a life lived long and plentiful, because this life is the only chance we get. I do not dare give myself the false comfort of an afterlife for these innocents , because that somehow lessens the impact of what has happened to them. I hear how they are in "a better place" now. Indeed, they no longer suffer, but no, it is not a better place. They have ceased to exist, no more than stardust in the memory of the universe. The finality of that gives me pause in a way "playing with the angels" and being "with their Savior" does not. It generates a much more urgent need (in me, at least) to address the issues that brought about this act of senseless violence and rage.
There are those who would say our failure to allow prayer in schools is to blame and some deity (insert your choice here) is bringing judgment on our country. I even saw a post about how a small child said the Christian God would protect her private school because they prayed every morning. For those of you to whom the logical failings of this are NOT obvious, I offer this: Any suggestion that an omniscient, omnipotent, all loving "God" would answer the prayers of one set of children over the cries for help of another set is complete bollocks. That would require a rather great number of exceptions to the laws of physics and general relativity, not to mention the biological pathways that would require rerouting in "real time" to ensure the perpetrator of mass murder shoots the right kids. It sounds ridiculous because it is. No god caused this problem, and I can assure you, no god will solve it.
I do not believe that better gun control is the answer. I do not think the failure to properly parent is the explanation. I do not think any response that lays blame on an arbitrary organization like the NRA is appropriate. It will not be until we, as a society, are willing to step up and take collective blame for our failure to ACT that we will see change. We must accept our own failings and work to alter our current reality.
As it stands, there are few doctors/psychologists/psychiatrists who stand ready to acknowledge that a child can be anything but good, decent and innocent. Countless parents (and I know some of them) struggle with the idea that their child is different, not quite right, even dangerous and exhaust all resources, both financial and emotional, trying to find some way, any way to get their children help. Society blames these people for not being better parents, for not putting their guns away, for not paying enough attention, for not knowing what the hell to do! These children are given every excuse in the world: they MUST be victims of abuse, they MUST have suffered some trauma, they MUST NOT be to blame. Right up until they turn 18, and all hope of actually helping them is lost forever, they are shunted from group to group, doctor to doctor, with no one willing to say that they are simply not normal and should remain under constant care and observation. No, these disturbed individuals are not to blame for their conditions. There is an underlying neuropathology that science simply does not yet have the tools to understand. It is no one's FAULT that these people are the way they are. It is OUR FAULT that we choose to ignore the reality that is before us. So I will say it now: not everyone deserves a chance at a "normal" life. Not everyone should be allowed to mingle with society. Sometimes it is in the best interest of an individual AND society for that person to be removed and cared for in a remote place, in such a way as to ensure their safety and the safety of others. Life, liberty and individual freedom for all is simply not possible sometimes, and the sooner we embrace that notion, the better off we're going to be.
Once we come to terms with the idea that some people are really and truly, at their core, not okay, then we can start to take steps to ensure those people get the help they need to live as close to a normal life as can be considered SAFE for the rest of us. We cannot address the problem until we acknowledge it exists. We cannot develop the programs and do the research that will help us explain the pathology of what happens to these individuals until we recognize that something IS happening to them and it isn't typical.
Doing the work I do, I am literally surrounded by the most brilliant minds on earth. The scientific community is a small one, and we all hit a basal level of intelligence. The truly intelligent, stand-out minds are easy to identify, because they aren't like the rest of us. They think differently; they work differently; they function in a way that is entirely other from the rest of our community. I would venture that most scientists and engineers function in a slightly different way from, say, folks in the humanities, but when there's a stand-out from the stand-outs, somebody better start paying attention.
These shootings are not the fault of parents, juvenile courts, the educational system or gun enthusiasts...they are the fault of all of us, for refusing to acknowledge the truth, in the hopes that we wouldn't have to pay the price. Well, news flash, the bill just came due and there are no refunds.
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