Optimistic Science Fiction

[Giovanni Lostumbo]

Saw this article coincidentally while reading about sci-fi authors like Isaac Asimov and Arthur C. Clarke yesterday. I thought it would be a good counterbalance to some of the anxieties posted here about garage biology, but also to consider biology research from the context of outerspace, and not just terrestrial milieus, yet still able to benefit terrestrial life/matters.

"Neal Stephenson on Science Fiction, Building Towers 20 Kilometers High ... and Insurance" :

http://www.technologyreview.com/blog/editors/27775/

[Cory Geesaman]

The guy hasn't really made any good sci-fi and seems to be making an attempt to hype up whatever his upcoming works are by getting his name out.  It would be cool if movies started coming out to make the common person less resentful toward people pursuing science - there has been a lot of trash coming out lately that seems to be making an attempt at turning people of different intellectual capabilities against one another, possibly only as an aside to the whole excuse of "some people are just smarter" that keeps many from even making an attempt to further themselves.

[Ainsley]

He wrote Snow Crash... not good sci-fi?

I guess it depends on your definition...

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[Cory Geesaman]

I'd never heard of it - just got it on the Kindle store to see what it's like.

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[mad_casual]

I've read both the Cryptonomicon, which was more historical fiction than science fiction and Anathem. I've certainly read worse fiction from more famous authors. I think we can all agree that Stephenson's best work is more worthy of the purchase, reading, and reproduction on the silver screen than, say, Dan Brown's best or another of Tom Clancy's works.

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[Cory Geesaman]

lol, Tom Clancy's works are all around terrible - I do like the premise of Snow Crash from what I saw in the first section of the wiki article on it (didn't read further because it seemed worth reading the actual book in spite of the Apple-jargon-derived name).  I read a lot of sci-fi so I took the fact I had never heard of this particular author before today as a sign he wasn't making a huge impact in the area.  I don't think the stance of sci-fi encouraging/discouraging scientists holds a lot of merit (if you are curious about the world around you and you have the competence to try you are going to do so regardless of the perception of what will come of it when/if a question ever leads to a technology of some form) - but in terms of how other people perceive science (and the political/legal ground we have to work in) it may make an impact.

[Tom Randall]

Some real science fiction, from today's issue of Science. Hope most of it comes through, graphics may not.

Science 20 April 2012:
Vol. 336 no. 6079 pp. 307-308
DOI: 10.1126/science.1221724

• Perspective

Evolution

Toward an Alternative Biology

1. Gerald F. Joyce

+ Author Affiliations

1. Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Related Resources

In Science Magazine

• Report Synthetic Genetic Polymers Capable of Heredity and Evolution

  • Vitor B. Pinheiro et al.

  Science 20 April 2012: 341-344.

Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution. It involves the storage and propagation of molecular information and the refinement of that information through experience and differential survival. Heretofore, the only molecules known to be capable of undergoing Darwinian evolution were RNA and DNA, the genetic molecules of biology. But on page 341 of this issue, Pinheiro et al. (1) expand the palette considerably. They report six alternative genetic polymers that can be used to store and propagate information; one of these was made to undergo Darwinian evolution in response to imposed selection constraints. The work heralds the era of synthetic genetics, with implications for exobiology, biotechnology, and understanding of life itself.

XNA analogs of nucleic acids.

DNA is composed of a deoxyribose–phosphate backbone and the standard four bases (A). Pinheiro et al. show that through transcription using engineered polymerases, DNA can be copied to various XNAs that are analogs of the DNA structure (B). Black, red, and green balls indicate carbon, oxygen, and fluorine atoms, respectively. These XNAs can in turn be reverse transcribed to DNA using other engineered polymerases. The current XNA amplification process relies on PCR amplification of a DNA intermediate (C).

These first steps outside of biological genetics are modest ones, involving XNA molecules, where NA stands for nucleic acid and X refers to the sugar moiety or its substitute. The compounds are analogs of biological nucleic acids (see the figure, panel A). However, the sugar or sugar-like component is not the ribose found in RNA or the deoxyribose found in DNA. It has been replaced by a different five-carbon sugar (arabinose in ANA, 2′-fluoroarabinose in FANA), a four-carbon sugar (threose in TNA), a “locked” ribose analog in LNA, or a six-member ring structure (cyclohexene in CeNA, anhydrohexitol in HNA) (see the figure, panel B).

The study of XNAs has been inspired by the question of what was the first genetic polymer of life on Earth. Perhaps this was RNA, but it may have been a simpler structure that was more readily accessible through prebiotic synthesis (2). TNA and glycol nucleic acid (GNA) are prime candidates (3, 4). Another inspiration for the study of XNAs is their application as antisense agents that bind to and thereby inhibit the function of biological RNAs. All six XNAs studied by Pinheiro et al. bind to complementary RNA and DNA and are resistant to degradation by biological nucleases. Finally, construction of genetic systems based on alternative chemical platforms may ultimately lead to the synthesis of novel forms of life. For that goal to be realized, the XNA must be able to catalyze its own replication, without the aid of any biological molecules, and thus be capable of undergoing Darwinian evolution in a self-sustained manner.

Pinheiro et al. have made great progress in showing that various XNAs can function as synthetic genetic polymers, but they have not yet realized a synthetic genetic system. In their system, the XNAs are replicated by reverse-transcribing them to DNA, amplifying the DNA using PCR, and then forward-transcribing the DNA back to XNA (see the figure, panel C). Each step uses a polymerase; amplification takes place with DNA. Another recent paper showed the storage and propagation of genetic information in TNA, but there, too, amplification occurred with DNA (5).

The key innovation of Pinheiro et al. is their use of sophisticated protein engineering techniques to develop variant polymerases that are adept at copying information between XNAs and DNA. They show that XNA polymers containing more than 70 subunits and having almost any sequence can be copied to and from DNA, with an average fidelity per subunit ranging from 95% (for LNA) to 99.6% (for CeNA). These attributes are sufficient to carry out the directed evolution of functional XNA molecules. The authors demonstrate this process for HNA polymers, which they evolved in the laboratory to obtain functional molecules (aptamers) that bind tightly and specifically to a particular RNA or protein target.

Pinheiro et al. give some hint of what will come next. They have begun to apply the same protein engineering techniques to develop polymerases that can copy an XNA to its own complement or copy information between two different XNAs. So far, both FANA and CeNA have been copied to their own complement and CeNA has been copied to HNA, but these processes are much less efficient than copying information between XNA and DNA.

Future studies are likely to yield improvements of the various XNA-to-XNA copying reactions. It also seems only a matter of time before there will be the first reported “XNAzyme”—a catalyst composed of XNA rather than protein or standard nucleic acid. A key aim will be the development of XNAzymes that catalyze the templated joining of XNA oligomers and ultimately the polymerization of XNA monomers. Synthetic biology studies of XNA may never catch up to those involving RNA because the former require more challenging preparative and analytical procedures and do not benefit from the technical infrastructure that supports RNA research. However, the comparative biochemistry of various XNA systems is itself a worthy pursuit, enabling one to investigate principles of macromolecular structure, molecular recognition, and catalysis across a series of related chemical polymers.

Another important reason to pursue the development of functional XNAs is to obtain compounds with potential applications in materials science, molecular diagnostics, and therapeutics. Nucleic acid aptamers have been widely adapted for these purposes, but because RNA and DNA are susceptible to biological nucleases, they must be modified to withstand exposure to the natural world. XNAs are unnatural and would pass through the biosphere unscathed. The benefits of their unusual chemical properties must be weighed against their greater cost, both literally and with regard to operating in the uncharted waters of XNA biochemistry.

As one contemplates all the alternative life forms that might be possible with XNAs and other more exotic genetic molecules, the words of Arthur C. Clarke come to mind. In 2010: Odyssey Two, HAL the computer tells humanity: “All these worlds are yours” but cautions: “Except Europa. Attempt no landings there” (6). Synthetic biologists are beginning to frolic on the worlds of alternative genetics but must not tread into areas that have the potential to harm our biology.

[shreyans chordia]

Awesome post dude!  thank you :)       But I have one question.. Do any of these XNA's stimulate immune response from our body?  Because that is one of the major challenges for the aptamer application in humans.

[Chris Templeman]

I was at the lecture / interview. It was great. I think Neal has a lot to offer the science community and I have been a fan of his work for a while. Relevant to this group I would recommend one of his first novels 'Zodiac' about a biohacker who fights to stop pollution in Boston harbor.

[Daniel C.]

On Fri, Apr 20, 2012 at 12:28 PM, Cory Geesaman <co...@geesaman.com> wrote:
> The guy hasn't really made any good sci-fi and seems to be making an attempt
> to hype up whatever his upcoming works are by getting his name out.

I think you're making the mistake of assuming that, because you
haven't heard of him, he's not a good author or not significant in his
field. He happens to be one of my favorite authors; I had to take a
few minutes to calm down before responding ;-)

Snow Crash was a pretty significant work when it came out - Time has
it on its list of the 100 best English-language novels since 1923
(when TIME Magazine started) along with Slaughterhouse Five, Animal
Farm, Gone With the Wind, Lolita, and others:
http://entertainment.time.com/2005/10/16/all-time-100-novels/#snow-crash-1992-by-neal-stephenson

The Diamond Age is sci-fi, and won Hugo and Locus awards and was
shortlisted for the Nebula award. Anathem is another sci-fi work
which got somewhat mixed reviews, but was #1 on the NYT bestseller
list (in the Hardcover Fiction category) and won the Locus Award for
best sci-fi novel in 2009, was nominated for the Hugo and other
awards, and is one of the few books to have been reviewed in Nature:
http://www.nature.com/nature/journal/v456/n7221/pdf/456446a.pdf

He also wrote Cryptonomicon, which isn't (exactly) sci-fi but is one
of my favorite novels. Also, when he spoke at MIT the other day (I
couldn't attend because I had prior obligations) the room was filled
to capacity. So while you may not like his work personally (which I
would certainly respect - different strokes and all that) I think it's
hard to support your statement that he hasn't made any good sci-fi.

-Dan

[Cory Geesaman]

I just finished reading Snow Crash in full and feel I've wasted significant hours of my life in doing so - would not recommend this book to anyone for the following reasons (in no particular order):

-It appears to be ghost-written, there are 2-3 distinct writing styles, all of them right around the 6th grade reading level (with multiple phonetic typos, grammatical errors and misplaced words/punctuation marks throughout, there are entire chapters that read like "see spot run" with technical jargon tossed around haphazardly to make it sound more intelligent than it is).

-It has more liberal subtext than all of Ann Rand's works have conservative/libertarian combined (The book is set in the recent past [based on the ages of characters relative to fixed dates] to an apocalyptic theme that could be drawn from the liberal scare-tactics of the early 90's).

-The underlying theme throughout (best highlighted in the conversation between the main good hero [Hiro] and the main bad hero [Raven] on their bike-race through the meta-verse) is that no matter how closely you can relate to someone, you cannot alter their actions - they will do what they will do without any form of reason or rational thought applied.

-The mythological basis is often misrepresented when citing actual mythos, completely ignoring mythical stories that could actually be used to represent the underlying concepts of the book.

-The book ends with a scene akin to the Futurama episode "Jurassic Bark".

-All the sci-fi type themes are lifted directly from previous stories (there is no visionary sci-fi in the book whatsoever).

-The multiple forms of ghetto-speak are more cumbersome to read through than the description of the para-people in "The Gods Themselves" (if this was done to illustrate the diversion of languages over time, it could have been done much better just by citing the multiple languages already in existence without becoming become nearly as tedious to interpret as "An Inquiry into the Nature and Causes of the Wealth of Nations").

-The character names are unimaginative placeholders that never seem to have been replaced (Hiro Protagonist, Y.T., etc) or names resembling mythical figures changed in such a manner as to suggest the original intent of the book (or perhaps just that of one of the ghost-writers) was that the mythical figures were coming back in the more modern characters of the book.

-About 50% of the book, when taken from the whole, is repetitive, adding nothing but filler (no additional descriptions of scenes, plot or personality type - just repetition).

-The author has likely never seen a thesaurus in his/their life/lives.

-The incredibly narrow perspective outlined in the book can be seen a good deal in the interaction with the "Librarian" program, who only cites 3-4 equally biased authors over the course of much (again, tedious and repetitive) dialog.

Again, I wouldn't recommend this book to anyone - not worth the $10, or even the time it takes to commute to the library, let alone read.  I definitely should have gone with my first instinct: title=Apple Jargon=Bad.

[Daniel C.]

On Sun, Apr 22, 2012 at 9:46 PM, Cory Geesaman <co...@geesaman.com> wrote:
> I just finished reading Snow Crash in full and feel I've wasted significant
> hours of my life in doing so - would not recommend this book to anyone for
> the following reasons (in no particular order):

You clearly have more refined taste than the editors of TIME Magazine,
and the members of the World Science Fiction Society (who grant the
Hugo Award). I hope you'll set the record straight next time you're
invited to speak at MIT.

-Dan

[Cory Geesaman]

lol - Yes, and I'm sure Siskel and Ebert do more than they are paid to do as well :)

[Daniel C.]

So not only is Stephenson a crappy author, but you're on par with
Siskel and Ebert. Fabulous.

I'm curious - you said that all of the sci-fi themes were lifted from
previous works. Which themes, and where were they lifted from? Were
you aware that Snow Crash was published in 1992? I'm just asking
because you compared the ending to a Futurama episode which aired in
2002. Incidentally, the episode you compared it to was nominated for
an Emmy - which kind of contradicts your whole "this book sucks"
thing.

-Dan

[Cory Geesaman]

There were a host of outer limits episodes in the 60's detailing the whole language as a form of control theme (the theme actually goes back in many occult texts to around 500BC - which I would consider early sci-fi) - I'm guessing you can find the rest readily enough from your own experiences reading sci-fi if you have read, well any, since control via language is by far the most obscure thing in the book (and frankly, seems like the author just looking through the fourth wall to kill the book in most of the areas it is cited).

I wasn't actually aware the Futurama episode was nominated for an Emmy (goes to show how low-quality formal rating systems are) - the reception amongst fans was pretty much unanimous - the episode was terrible and depressing (though maybe that's just what qualifies for these awards - when standard marketing techniques just won't suffice).

I wouldn't consider myself on par with Siskel and Ebert - my opinions aren't for sale.

[Giovanni Lostumbo]

One thing that is worth differentiating is that even if an author is subjectively a "bad" or "terrible" writer, he or she can still make an insightful and much needed social commentary on the state of science fiction, which is largely fearsome and pessimistic. If anyone wanted to change that literary atmosphere, it requires someone to come forward to admit that, and in this case Stephenson admits his own works were prone to this tendency too. The merits of one's views, no matter how mediocre one's larger body of works are, are always independent and equally subjective to their other contributions. I guess it depends on how one wants to group intent. A quote by Carl Woese: "All the junk written about Beethoven's irascible personality does not add at all to the appreciation of his music." In this case, Stephenson is a social commentator with appreciative, sound opinions, the way someone else might appreciate Beethoven's sounds (A bit of a play on words there;). Maybe he's trying to compensate by being the workhorse amongst his peers. In any case, meritocracy has flaws, because opinions shouldn't carry weight based on one's status in society, considering it can be completely unrelated to their specialty. It shows why free speech, and anonymized opinions on an online forum allow more diverse views to be heard (pending the screening of dominant trolls), ideally with proportional representation from the demographics of the wider population. Any minority opinion is susceptible to the tyrrany of a majority opinion.

[David Murphy]

Personally I thought snow crash was pretty awful but with a few good points mixed in.

Love the diamond age though. the end kind of falls flat and at points the writing is poor but the world he builds is wonderful beyond measure.

I would highly recommend Interface by Neal Stephenson and George Jewsbury. They seemed to compliment each other well.

 

 

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[NB]

I am wading into this firefight in the interest of science fiction, an art form that has always been divisive, in fact often deliberately so. The reason sci-fi is a persistent, fresh genre is that it provokes exploration of society and technology in relevant and dynamic ways. Not only are the author's literary practices of merit, so are their conceptual explorations of the interaction between technology and man. Technology can range from social technology to literal silicon and spaceships, and therefore the genre is quite broad and ever evolving. One unifying trend between sci-fi works is the humanization of the challenges of "progress." From exegetics to open discussion in a work, sci-fi can presciently develop new ideas, espouse caution, or popularize innovation via inspiring individuals outside of the literary intelligentsia. The Science Fiction Hall of Fame has excellent treatment of the myriad manifestations of sci-fi, a genre that challenges simple characterization.

For example, Arthur C. Clarke is often credited as seminally promoting GPS. When an author wades into the intersection of science and literature (Clarke famously did both professionally), s/he may is not simply judged for doing it first. The merit is also in the quality and reach of such creative treatment of innovation. This reach of influence is supremely relevant. Apple did not invent the MP3 player; they just did it transformationally better. The benefit of being first vs. best to market is a subject of debate in the innovation and business communities for a reason.

Snow Crash is an indisputably influential book. Regardless of the opinions of individual readers, the fact is, it embodied and influenced a generation of readers who went on to translate these concepts. These individuals developed landmark technologies and acknowledged the role of the book in either directly inspiring their ideas, or catalyzing their work to make them a reality. A book influencing so many people, of such notable caliber, cannot simply be dismissed.

Snow Crash has always been divisive due to its style, a "love it or hate it" book. The "main characters are embodied ideas or ideologies." Over the top (in some opinions) names and puns are part and parcel of the author's style, and are valid forms of writing. Style can be critically discussed in a productive fashion, impact is a separate issue. Stylistic criticism would be more at home in literary circles.

If a critic will espouse heated personal opinion, the basis for plenty of artistic criticism, it is worthwhile to be informed of the subject matter and logical fallacies that undermine such arguments. Moreover, when discuss other ideologue writers, such as Ayn Rand, it is best to properly spell the author's name, and to be aware of the explicit nature of her philosophy in works such as Atlas Shrugged. Atlas Shrugged is both a longer book, and a more overt ideological vessel in many respected critical opinions.

TLDR: Just because you don't like it, doesn't make it fact. Strive for informed opinions, based on rational research and tolerance of individual viewpoints. Test the merits of your trolling in the appropriate venue (literary criticism publication) and see how they are received.

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[mad_casual]

On Friday, April 20, 2012 2:55:47 PM UTC-5, Cory Geesaman wrote:

lol, Tom Clancy's works are all around terrible - I do like the premise of Snow Crash from what I saw in the first section of the wiki article on it (didn't read further because it seemed worth reading the actual book in spite of the Apple-jargon-derived name).

Got any opinions on Dan Brown's work(s)?

[Cory Geesaman]

Send me a private message via email if you're interested in discussing it - I don't want to pollute the group with too much discussion that's off-topic from the DIYbio theme (I tend to favor sci-fi, research papers and technical manuals - I'd consider the The Da Vinci Code pretty bad for reasons you may not even relate to and they aren't entirely based around writing style).

[mad_casual]

Sorry, wasn't looking for a treatise, just curious as to the criticism of Stephenson and Clancy, but not Brown.