Tag Archives: Technology

Progressing the Person and Policy

The English word “person” has a long and convoluted history. Though the word itself likely derives from the Latin, persona, referring to the masks worn in theatre, its meaning has evolved over time. One of the biggest conceptual overhauls came in the 4th century AD during a church council that was held to investigate the concept…

via Progressing the Person and Policy — Savage Minds

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Artificially Intelligent, Genuinely a Person

It’s difficult to overstate our society’s fascination with Artificial Intelligence (AI). From the millions of people who tuned in every week for the new HBO show WestWorld to home assistants like Amazon’s Echo and Google Home, Americans fully embrace the notion of “smart machines.” As a peculiar apex of our ability to craft tools, smart…

via Artificially Intelligent, Genuinely a Person — Savage Minds

Medicine, Technology, and the Ever-Changing Human Person

Though we often take for granted that humans are persons, they are not exempt from questions surrounding personhood. Indeed, what it means to be a person is largely an unsettled argument, even though we often speak of “people” and “persons.” Just as it’s important to ask if other beings might ever be persons, it is […]

via Medicine, Technology, and the Ever-Changing Human Person — Savage Minds

Multiplex Automated Genome Engineering: Changing the world with MAGE

Humans have evolved a most unique mastery of toolmaking through advanced technology. As an extension of our biological bodies, technology has loosened the grip of natural selection. This is particularly true in the field of biomedicine and genetic engineering. We have the ability to directly alter the blueprint of life for any purpose we wish. Beginning in the 1970’s with the creation of recombinant DNA and transgenic organisms, genetic engineering has offered scientists the ability to study genes on a level that may not have seemed possible at the time. The field has provided a wealth of knowledge as well as practical implications, such as knockout mice and the ability to produce near-endless amount of human insulin for diabetics.

As of 2009, multiplex automated genome engineering (MAGE) has ushered in a new branch of genetic engineering – genomic engineering. We are no longer restricted to altering single genes, but rather are able to alter entire genomes by manipulating several genes in parallel. This new ability, brought about by MAGE technology, allows for nearly endless applications that stretch well beyond medicine or industry; agriculture, evolutionary biology, and conservation biology will benefit tremendously as MAGE technology progresses. Genetic engineering advancements such as MAGE are poised to revolutionize entire fields of science, including synthetic biology, molecular biology, and genetics by offering faster, cheaper, and more powerful methods of genome engineering.

Homologous Recombination

Genetic engineering underwent a revolutionary change in the 1980’s, largely due to the pioneering work of Martin Evans, Mario Capecchi, and Oliver Smithies. Evans and Kauffman were the first to describe a method for extracting, isolating, and culturing mouse embryonic stem cells. This laid the foundation for gene targeting, a method that was independently discovered by both Oliver Smithies and Mario Capecchi. Mario Capecchi and his colleagues were the first to suggest mammalian cells had the machinery capable for homologous recombination with exogenous DNA. Smithies took this a step further, demonstrating targeted gene insertion using the β-globin gene. Ultimately, the combined work of Evans, Smithies, and Capecchi on homologous recombination earned them the Nobel Prize in Physiology or Medicine in 2007. The science of homologous recombination has allowed for many scientific discoveries, primarily through the creation of knockout mice.

Homologous recombination works under many of the same principles are chromosomal recombination in meiosis, wherein homologous genetic sequences are randomly exchanged. The difference lies in the fact that homologous recombination works with exogenous DNA and on a gene level rather than chromosomal level.

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The method works by using a double stranded genetic construct with flanking regions that are homologous to the flanking regions of the gene of interest. This allows for the sequence in the middle, containing a positive selection marker and new gene, to be incorporated. The positive control should be something that can be selected for, such as resistance to a toxin or a color change. Outside of one of the flanking regions of the construct should lie a negative selection marker; the thymidine kinase gene is commonly used. If homologous recombination is too lenient, and the thymidine kinase gene is incorporated into the endogenous DNA, it can be detected and disposed of. This is to prevent too much genetic information from being exchanged.

Using this method, knockout mice can be created. A knockout mouse is a mouse that is lacking a functional gene, allowing for elucidation of the gene’s function. Embryonic stem cells are extracted from a mouse blastocyst and introduced to the gene construct via electroporation. The successfully genetically modified stem cells are selected using the positive and negative markers. These are isolated and cultured before being inserted back into mouse blastocysts. The mouse blastocysts can then be inserted into female mice, producing chimeric offspring. These offspring may be mated to wild-type mice. If the germ cells of the chimeric mouse were generated from the modified stem cells, then the offspring will be heterozygous for the modified gene and wild-type gene. These heterozygous mice can then be interbred, with a portion of the offspring being homozygous for the modified gene. This is the beginning of a mouse line with the chosen gene “knocked-out.”

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Multiplex Automated Genome Engineering Process

The major drawback of the previously described method of “gene targeting” is the inability to multiplex. The process is not very efficient, and targeting more than one gene becomes problematic, limiting homologous recombination to single genes. In 2009, George Church and colleagues solved this issue with the creation of multiplex automated genome engineering (MAGE). MAGE technology uses hybridizing oligonucleotides to alter multiple genes in parallel. The machine may be thought of as an “evolution machine,” wherein favorable sequences are chosen at a higher frequency than less favorable sequences. The hybridization free energy is a predictor of allelic replacement efficiency. As cycles complete, sequences become more similar to the oligonucleotide sequence, increasing the chance that those sequences will be further altered by hybridization. Eventually, the majority of endogenous sequences will be completely replaced with the sequence of the oligonucleotide. This process only takes about 6-8 cycles.

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After the E. coli cells are grown to the mid log phase, expression of the beta protein is induced. Cells are chilled and the media is drained. A solution containing the oligonucleotides is added, followed by electroporation. This step is particularly lethal, killing many of the cells. However, the cells are chosen based on positive markers (optional, but increases efficiency) and allowed to reach the mid-log phase again before repeating the process. Church and his colleagues have optimized the E. coli strain EcNR2 to work with MAGE. EcNR2 contains a plasmid with the λ phage genes exo, beta, and gam as well as being mismatch gene deficient. When expressed, the phage genes will help keep the oligonucleotide annealed to the lagging strand of the DNA during replication, while the mismatch gene deficiency prevents the cellular repair mechanisms from changing the oligonucleotide sequence once it is annealed. Using an improved technique called co-selection MAGE (CoS-MAGE), Church and colleagues created EcHW47, the successor to EcNR2. In CoS-MAGE, cells that exhibit naturally superior oligo-uptake are selected for before attempting to target the genes of interest.

MAGE technology is currently in the process of being refined, but shows incredible promise in practical applications. Some of the immediate applications include the ability to more easily and directly study molecular evolution and the creation of more efficient bacterial production of industrial chemicals and biologically relevant hormones. Once the technique has been optimized in plants and mammals, immediate applications could be realized in GMO production and creation of multi-knockout mice that will give scientists the ability to study gene-gene interactions on a level previously unattainable. A more optimistic and perhaps grandiose vision could see MAGE working towards ending genetic disorders (CRISPR technology, an equally incredible genomic editing technique, may beat MAGE there) and serving as a cornerstone technique in de-extinction. The ability to alter a genome in any fashion brings with it immense power. The possibilities for MAGE are boundless, unimaginable, and are sure to change genomic science.

For more information on Homologous recombination, see:

http://www.bio.davidson.edu/genomics/method/homolrecomb.html

For more information on MAGE, see:

Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009). Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257), 894-898.

Wang, H. H., Kim, H., Cong, L., Jeong, J., Bang, D., & Church, G. M. (2012). Genome-scale promoter engineering by coselection MAGE. Nature methods, 9(6), 591-593.

For more information on CRISPR (which I highly recommend; it’s fascinating), see:

https://www.addgene.org/CRISPR/guide/

The Role of Science in Society

Introduction

Carl Sagan once stated, “… the consequences of scientific illiteracy are far more dangerous in our time than in any time that has come before.” This statement becomes truer every day, as scientific and technological innovations are occurring at an ever-increasing rate. Studies suggest that less than 30% of Americans are “scientifically literate,” meaning that over 70% of Americans would have trouble reading – and understanding – the science section of the New York Times. So, why is this important? After all, everyone has their strengths and weaknesses.

The problem with this view is that science is a driving force behind our sociocultural evolution. New ideas and new inventions are constantly redefining how we live our lives. As time goes on, science and technology will define most of life as we live it. Already, this is true. 100 years ago, people often lived day by day without electricity. Today, the most frightening thing most people could imagine would be a total loss of electricity. Imagine all of the things that simply wouldn’t work without it: phones, televisions, the Internet, lighting, heat and A/C, automobiles, and many parts of the manufacturing process for everyday items. We have built a society in the United States that is almost entirely dependent upon electricity. Personally, It’s difficult for me to imagine a world without electricity because everything I know is based on upon it. Life has become relentlessly complex and multifaceted. Most people have no idea how the world around them – that is, this semi-artificial world, or anthropogenic matrix – functions.

As time goes on, our day-to-day lives will become less and less “natural” and more and more artificial. This is not inherently bad. However, it does raise the standards for what we must understand about how the world, especially our anthropogenic matrix, works. Failing to keep a basic understanding of science and technology is destined to segregate the population, facilitating the rise of an “elite” few, resembling more of an oligarchy than a representative democracy. I’m not much of a conspiracy theorist, and I don’t mean to imply that a “New World Order” is going to secretly control our lives. I do, however, think that if nothing is done about our general ignorance of science, we will slip away from the democracy that we claim to love so dearly. How? How can ignorance of science and technology lead to the failure of democracy? After all, you can vote regardless of your scientific literacy. While it’s true that you can vote while being largely ignorant of how the world works, this is part of the problem. To be clear, I do not think that there should be any kind of scientific literacy test in order to vote. This would only serve as fuel for the ever-broadening gap between those who understand science and those who don’t. In a democracy, everyone should be able to vote. However, given the state of knowledge that we currently have and the increasingly complex world in which we find ourselves, uneducated voting has disastrous consequences.

A Little Politics

Politics is, in its most basic form, the practice of influencing a population. This is done by verbally persuading people to get behind an action that will be set in motion order to guide the population down a particular path of life. The United States is a representative democracy, which means officials are elected by the public to govern the public. The United States is not a simple representative democracy; many modifications are set in order to give the minority a voice. However, in light of these modifications, “majority rules” is still the rule of thumb. On its surface, a “majority rules” system seems ideal. Going with what most people want or believe is the best thing to do seems like a solid idea. I agree that this is typically a good philosophy – that is, as long as those voting are educated on the matter at hand.

The Modern Intersection of Science and Government

The base of everything in our lives is built from science; it holds together our infrastructure. When a politician makes a motion to change or regulate something, he or she is making a change that affects our anthropogenic matrix, and, consequently, the natural world in which our matrix operates through such acts as deforestation, ozone depletion, species extinction, etc. If a constituent does not have a basic understanding of how the world works, then how can that individual make a good decision with regards to electing a public official who will pass laws that affect the world? Moreover, ignorance of science and technology (not to mention poor reasoning and logical evaluation skills that tend to accompany science education) leads to a vote based largely on emotion and superficial similarity. If you know very little about a subject, you cannot make an educated decision regarding that subject. If not based on an educated understanding, something else must be the base upon which you make decisions. The next best choice would be decisions based on reason and logic. Unfortunately, a fostering of critical thinking is also aloof in many educational settings. Science acts as a major source of training by which people learn to reason and form logical conclusions. In turn, many – though not all – who base their decisions on logical reasoning are in the same group of people who base their decisions on knowledge of science.

If you don’t use a knowledge of science to aid in political decision-making, it’s likely that you are more swayed by charisma and emotional triggers. Those candidates who are more like you, or at least are ostensibly like you, are more likely to sway your opinion. After all, that’s what politics is all about – persuading people. If most of your constituents are not scientifically literate, then you as a politician will be less likely to use science as a persuasion tactic and more likely to use charisma and emotionally charged wording that resonates with many of your constituents. Though not a valiant method of persuasion, it is a smart one. Unfortunately, this only perpetuates the current epidemic of scientific illiteracy.

Why Public Knowledge of Science Matters

One major problem with scientific illiteracy is that politicians can make a poor decision, intentionally or unintentionally, with no one to call them out. Regulations or the lack thereof concerning issues such as climate change, medical research, and irresponsible use of resources must be made based on the science that is used to study and understand these matters. If a politician uses a non-scientific basis for creating laws (a basis fueled by a constituency who is scientifically illiterate and, perhaps, an ulterior motive such as monetary stock in the decision), then consequences are sure to ensue. The effects can be immediate, such as lack of funding for education or medical research, or delayed, as with the consequences surrounding anthropogenic climate change.

Politics aside, understanding science and technology is imperative to functioning in our ever increasingly technological world. 100,000 years ago, one had to be a skillful hunter or gatherer; 10,000 years ago, one needed to be adept in agriculture; today, we must stay informed on, at the very least, the basics of science. Expertise is not required for social and political progress, but awareness is essential.