#23. A Summary of ‘Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves’ by George M. Church and Ed Regis

Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves by George M. Church and Ed Regis

‘Regeneis: How Synthetic Biology Will Reinvent Nature and Ourselves’ by George M. Church and Ed Regis (Basic Books; October 2, 2012)

Table of Contents:

i. Introduction/Synopsis

PART I: AN INTRODUCTION TO SYNTHETIC BIOLOGY

1. Understanding DNA: The Basics

2. Reading DNA

3. The Evolution of Synthetic Biology: Gene Modification and Creation (From Splicing to Writing)

4. The Standardization of Synthetic Biology: Biobricks

PART II: THE APPLICATIONS OF SYNTHETIC BIOLOGY

5. IGEM

6. Bioenergy: Bioelectricity and Biofuels

  • a. Bioelectricity
  • b. Biofuels

7. Biomaterials: Biochemicals and Bioplastics

  • a. Biochemicals
  • b. Bioplastics

8. The Future of Biomaterials and Engineered Organisms: Mirror Biology

9. Biomedicine

  • a. Diagnostics
  • b. Drugs and Treatments
  • c. Vaccines and Immunization
  • d. Engineering the Human Genome

10. Paleo-Cloning: Resurrecting Extinct Species

  • a. The Pyrenean Ibex
  • b. Woolly Mammoths and Beyond

11. Moving Forward in Synthetic Biology: DIY Biology

12. Conclusion

 i. Introduction/Synopsis

DNA was only discovered about a century ago, and it’s structure remained a mystery until about half a century ago, but since this time our knowledge and understanding of DNA has grown immensely (indeed exponentially). What’s more, this understanding has evolved to include not just an understanding of how DNA works, but also how it can be manipulated to help advance our ends. The most glaring example here is the phenomenon of genetically modified food. Though not without controversy initially (and some fringe opposition that lives on to this day), it is fair to say that genetically modified food was one of the major scientific advances of the 20th century. Over and above this, our understanding of DNA appeared to reach its most impressive manifestation with the successful sequencing of the human genome in the year 2000.

For the genetics professor and pioneering genetic engineer George Church, however, genetically modified food and the Human Genome Project are but the tip of the iceberg when it comes to the potential of genomics. Indeed, since the year 2005, the exponential growth rate in our ability to read and write DNA has increased from 1.5-fold per year (a rate that matches Moore’s law), to the incredible rate of 10-fold per year (p. 243). This explosion in scientific and technological progress has resulted in dramatic advancements in the areas of biochemicals, biomaterials, biofuels and biomedicine. What’s more, advancements in these technologies are but in their incipient stage, and the future of genomics promises to dwarf these initial achievements. In their new book Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves George Church and science writer Ed Regis take us through the developments that have occurred recently in the area of genomics, and also where these developments are likely to take us in the future.

When it comes to the current state of the field, manipulating DNA has already allowed us to produce organisms with new features, such as foodstuffs with novel properties, greater productivity and nutritional value, and resistance to pathogens. Over and above this, micro-species have been programmed to do such things as detect impurities in drinking water, produce electricity from wastewater (and purify the wastewater in the process), produce blood, produce vaccines, take pictures, and even store information. Indeed, the potential to use DNA as a store of information is already recognized to be the likely next leap in computer science, and is poised to initiate a revolution in informatics (just imagine storing all of the information in Wikipedia [in every language] on a chip the size of a blood cell, for a cost of $1 for 100,000 copies).

And, of course, the potential to manipulate genomes does not end with other species: it can also be extended to our own. Actualizing this potential is not far off, and includes such things as increasing intelligence, gaining full immunity to any pathogen (real or hypothetical), and dramatically extending the lifespan (if not eradicating mortality altogether).

In addition to manipulating genomes for the purpose of creating organisms with new biological features, the productive capacity of the genome can also be exploited to produce new substances and materials, such as chemicals, plastics, fuels, drugs, and vaccines. Successes in each of these areas has already been achieved, and the field is on the cusp of scaling-up these processes to an industrial scale. What’s more, manipulating genes shows the promise of expanding the current repertoire of the building blocks of substances and materials to produce a whole new array thereof.

Here is Dr. Church in a TED talk from 2010 discussing some recent advances in synthetic biology:

What follows is a full executive summary of Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves by George Church and Ed Regis.

PART I: AN INTRODUCTION TO SYNTHETIC BIOLOGY

1. Understanding DNA: The Basics

All of life’s complexity is derived from a very simple compound known as deoxyribonucleic acid (DNA), that lives in the nucleus of most living cells. In basic terms, an organism’s DNA provides the blueprint for how that organism converts food into proteins that make up the bulk of its cells, tissues, organs, vital fluids and ultimately systems that allow it to function, survive and reproduce. As Church explains, DNA “contain[s] the genetic information, the software of life. This software runs the cell in as literal a sense as a computer’s operating system runs the computer. It directs the formation of proteins. It contains the cell’s own recipe, the complete instruction set necessary and sufficient for making another nearly identical cell” (loc. 797).

It is important to note, however, that the end products that DNA creates are not determined by it alone, but by how the genetic material (or genes) interact with the environment: “genes and the environment interact to form the sum total of human individuality and variability/(as geneticists like to say, the genes may load the gun but the environment pulls the trigger)” (loc. 3916/3912). As a result of the interdependence of genes and the environment, there are “correlations… between genes… and observable traits such as eye color, hair color, facial features, cognitive abilities, eating habits, lifestyle, personal history and experiences, career choices, mental outlook and lots of other things” (loc. 3915).

Understanding just how we get from genes to traits is important in understanding how the science of synthetic biology works, and therefore, we will explore this process now. To begin with, the key elements of DNA are its bases (also called nucleotides), of which there are four: adenine (A), cytosine (C), guanine (G) and thymine (T) (loc. 614). These nucleotides link up with one another to form long chains of double-stranded DNA (called chromosomes). Adenine only links up with thymine, and cytosine only links up with guanine, thus the building up of a chain of DNA is a very simple and straightforward process (loc. 621).

DNA chromosme gene adenine thymine guanine cytosineIn order to create a protein to be used in biological functioning, a chain of DNA first splits down the middle, leaving two separate strands with unconnected bases. Another type of nucleic acid called ribonucleic acid (RNA) then comes along and reads the bases of the DNA strand, and assembles a complementary nucleic acid strand. As Church explains, “a molecule of RNA polymerase (an enzyme) unzips a section of double-stranded DNA, reads off its genetic information, and constructs a complementary strand of mRNA (messenger RNA), in a process called transcription” (loc. 874). RNA differs from DNA only in that the base thymine (T) is replaced by uracil (U) (which bonds with adenine). So a gene that runs AAGACTT will be read to build an mRNA strand that runs UUCUAA.   The messenger RNA is now ready to leave the nucleus of the cell and venture out into the cytoplasm where it will be involved directly in the creation of a protein.

Once out of the nucleus, the mRNA travels to an organelle in the cytoplasm called a ribosome, where the manufacturing of proteins takes place. The ribosome reads the mRNA three nucleotides at a time (these triplet nucleotides are called codons), and matches each codon with a conglomerate consisting of another chain of RNA (this time called transfer RNA, or tRNA) and an amino acid (which comes from digested food). This  process is called translation (loc. 877). While the number of nucleotide triplets (codons) tops out at 64, only 20 standard amino acids exist, and therefore, there is a good amount of redundancy in the translation from codons to amino acids (loc. 1343).

As the ribosome reads its way through the mRNA strand one codon at a time, the amino acids are collected together until, eventually, they are built up into a protein: “since a protein is nothing but a long string of amino acids, when the translation is complete, so is the protein” (loc. 877). The protein is then ready to be used within the cell itself, or shipped out of the cell to be used somewhere else in the body.

Here is an excellent video presentation of the aforementioned process:

2. Reading DNA

The general structure of DNA was only unravelled in 1953 (by Jim Watson and Francis Crick—a discovery that won the two a Nobel Prize [loc. 624]). However, it did not take long for biologists to learn how to read (or sequence) genomes. Indeed, this feat had been accomplished by the 1970’s (loc. 753). Sequencing genomes is important because, by matching up gene sequences with observable characteristics, biologists can learn how genotypes (genes) translate into phenotypes (traits), as well as susceptibility to diseases (loc. 1596, 3912).

*For prospective buyers: To get a good indication of how this (and other) articles look before purchasing, I’ve made several of my past articles available for free. Each of my articles follows the same form and is similar in length (15-20 pages). The free articles are available here: Free Articles

6 thoughts on “#23. A Summary of ‘Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves’ by George M. Church and Ed Regis

  1. Thanks for summarizing the book, adding links, and adding the videos. I just read the book, but your summaries are succinct and useful, and you added value through your links and videos.

  2. Thank you so much for this understandable review. I find bioengineering so so fascinating. But…
    I couldn’t quite synthesize Regenesis by George Church and Ed Regis. But, I really wanted to because of his personal experience with the Human Genome Project and Biogen. It was frustrating because there were so many real life examples, many performed by the professor himself, hidden in with the data.

    I also just got your How Science is Reinventing Life. If you have any new ones, please email me. I will be your first download.
    All the best to you. Heather

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