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Volume 24 Lent 2015
University of Cambridge
POLICY
Evidence-based
Policymaking
GENETICS
Epigenetics and
Lamarckian Inheritance
IMMUNOLOGY
The Immune System:
A cure for cancer?
SYNTHETIC BIOLOGY
The next revolution?
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TABLE OF CONTENTS
4
5
How should evidence affect
policymaking?
8
Message from the President
Cambridge features
5
Evidence-based Policymaking
and its Importance
Afham Raoof
8
Epigenetics and Lamarckian
Inheritance
Jane Phea
Cover Article
13
Synthetic Biology
The Next Revolution?
Hugh Wilson
16
A potential cure for cancer?
Wearn Xin Yee
Understanding the Immune System
Epigenetics saves Lamarck’s
theory of inheritance
INTERNATIONAL FEATURES
16
How the immune system
may ‘cure’ cancer
23
The Great Pacific Garbage Patch
Johns Hopkins
20
Implications of Synthetic Life
Sohail Zahid
Johns Hopkins
23
Why the World’s Largest Landfill
is in the Ocean
Stephen Jenkins
Cornell
26
The New “Black Gold”: Biochar
Jennifer Sun
Cornell
28
Reading Reinvented
How Computers and the Internet are
Inf luencing our Society
Latha Panchap
31Acknowledgements
THE SCIENCE IN SOCIETY REVIEW ∙ LENT 2015
INSIDE TTH
THE CAMBRIDGE TEAM
President
Justin Koh (Queens’)
Editors-in-Chief
Justin Koh (Queens’)
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Managing Editor
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Outreach DIrector
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Events DIrector
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Skill Development Officer
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Production Manager
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Assistant Production Manager
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Sponsorship Director
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Junior Treasurer
Maria Tang (St John’s)
SENIOR REVIEWERS
Dr Gos Micklem
A Message from the President
Happy New Year, everyone!
The Triple Helix is back for another term
of scientific perspective! This time, we
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form of technology—Biology! Who says
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endeavor, when some of the greatest
mysteries and potential lie are written in our
genes? Speaking of genes, look out for a fresh
perspective on why giraffes have long necks. (Hint: It’s not a tall
story.)
We also have an article on how our body may be greater than we
could ever imagine, where scientists are trying to discover ways to
exploit the immune system to treat cancer. That Zen quote about
“change must come from within” may just hold true in this respect.
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Dr Elizabeth Radford
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Justin Koh
Professor Anne Ferguson-Smith
President
The Triple Helix Cambridge
Łukasz Magiera
Dr Alex Morris
Journal design by Fred Zhu.
4
REPRODUCED FROM [8]
THE TRIPLE HELIX CAMBRIDGE
CAMBRIDGE
Afham Raoof
Evidence-based Policymaking
and its Importance
Afham Raoof is a second year Natural
Sciences student at Selwyn College.
He enjoys reading, quizzes, badminton and spending an inordinate
amount of time watching sports,
especially American ones. He hopes
to one day help make the world a
better and more sensible place.
E
vidence. The principle upon which all
scientific endeavour is founded. It has long
been undisputed that the analysis of evidence is integral to improved understanding of the world, and, especially in the case
of medicine, integral to the decision making process for issues that affect people’s lives. Yet the
use of evidence is not given its requisite importance in
the sphere where people are perhaps affected the most—
that of government policymaking. For too long, governments have worked upon predetermined principles, dependent on their political ideologies. I am advocating a
change in this approach, and an increased importance in
the role of evidence in policymaking.
5
CAMBRIDGE
what is evidence-based policy?
An evidence-based approach to policymaking is one
where governments attempt to gather data about the results of different courses of action, and thus determine
which course will be most beneficial for their citizens.
Governments often do not do this. Historically, they have
come in promising a broad range of ideas that all can be
defined under one political umbrella: “left”, “right”, “socialist”, “libertarian” or something similar. Political parties base their overall policy theme around what they
believe to be the values and beliefs of the electorate (or
what beliefs they think will best get them elected). However, representation is not the only important function
of governments. Another is creating the set of policies
that best helps all of their citizens. An evidence-based
approach, when possible, is the only way to achieve this.
It is extremely unlikely that the optimum set of policies
will all come from one part of the political spectrum.
Governments should seek out the best policies in a similar way to how scientists seek out the best theories—by
gathering evidence on multiple possibilities, and coming to a reasoned and considered decision. There are of
course some areas where such an approach is not feasible, and a moral or social judgement has to be made (the
definition of marriage being an obvious example). But
there are many where it is. Such an approach would also
help mitigate the petty arguing that so pervades politics
nowadays, as can be seen in the terrible behaviour by
MPs at Prime Minister’s Questions. Evidence promotes
the attitude of working together towards a problem,
rather than merely trying to prove your party’s ideas
are better than the other’s.
where can it be helpful?
The best example of where ideological policymaking
has been harmful is probably the drug war. Drug policy
lends itself to an evidence-based approach more than
other areas of government policy (as will be discussed
later). It is largely a medical issue that governments
have insisted as treating as a criminal or ideological
one. The harms of drug use to society are similar to the
harms caused by illnesses—personal misery, healthcare
costs, effects on families, etc. I will not get on my soapbox about drug decriminalisation here, but instead point
out that governments are not considering the right
variables. Fundamentally, as an issue of public health,
a cost-benefit based approach should be used. Governments should consider whether the immense cost and
effort spent on drug enforcement, combined with the
loss or benefit to those who either enjoy taking drugs
or are helped by them, is outweighed by the benefit to
society caused by the reduction in harm due to reduced
drug consumption. A similar approach is used by the
National Institute of Clinical Excellence when deciding
whether to fund a drug for the NHS. Instead the British
6
government punishes drug users to “send a message”
that they are wrong, as David Cameron said in 2014.
Making moral, ideological judgements on drug users is
not conducive to an overall increase in social welfare.
While I think it is obvious what the conclusion would
be if this analysis was carried out, that is not the issue.
The issue is that governments utterly refuse to consider the issue in these terms. The British government’s
refusal to consider evidence in this sphere is seen by
their sacking of Professor David Nutt as an advisor, after he attempted to suggest, evidentially, that the harms
of drugs such as ecstasy were not commensurate with
their penalties for consumption.1 Professor Nutt suggested that ecstasy was “no more dangerous than riding
a horse”, making a mockery of the government’s harsh
penalties for its possession. He was censured as a result.
It is extremely unlikely
that the optimum set
of policies will all come
from one part of the
political spectrum
alternate approaches
It is true, however, that not all areas of government policy lend themselves to such an approach as well. Friedrich Hayek, the 1974 Nobel Laureate in Economics,
mentioned in his Nobel speech the difficulty of applying
scientific methods to social sciences, saying “…in the
social sciences, often that is treated as important what
is available for measurement.”2 As the quote says, it is
true that in areas such as economics, obtaining reliable
evidence for the effects of such policies is extremely
difficult. A purely evidential approach is not possible
in these cases. Indeed, a government that has an agenda which it is able to pretend is evidence-based can be
extremely dangerous. A modification of the evidential
method is needed.
In this scenario, a Bayesian approach, where economic theories are modified depending on available evidence
weighted with a prior probability of this evidence occurring, would be the most sensible. Immigration is another
issue where while a purely evidential approach may not
be possible, it is still necessary to gather evidence and
consider the evidence available. Recent studies showing
the benefits of legal immigration to Britain3 should be
driving forces behind our policies, not anecdotes and
preconceived notions of what Britain should be like.
Equally, studies showing the negative effects of immi-
REPRODUCED FROM [9]
gration, if they were to be published, should be considered. Countries such as Sweden, which have liberal
immigration policies as a matter of principle,4 should
reconsider such ideas if they are found to be having a
negative impact on its citizens. The paramount principle
is simple. Governments must do what is best for everyone. Evidence is the best way to achieve this.
the current state of
evidence-based policy
It must be said that the use evidence-based policy is
in a much better state than it was even 20 years ago.
The government of Tony Blair explicitly set out the use
of evidence as one of its main plans, with Blair saying
in 1999 “We will ensure that all policies and programs
are clearly specified and evaluated, and the lessons of
success and failure are… acted upon”.5 Barack Obama
has also stated that he is in favour of such an approach.
However, it is extremely difficult to be confident in
the ability of governments to deliver on such promises when people who show ignorance of the most basic
science are given senior positions in government. In
America, a recent storm has broken out due to Senator
James Inhofe, a man who has previously said that global warming is “The greatest hoax ever perpetrated on
the American people”, likely being appointed chair of
the Environment and Public Works committee.6 Inhofe,
by his statements, has clearly shown himself unable to
sensibly analyse the vast corpus of evidence available in
favour of anthropogenic climate change. The fact that
the US Congress is willing to appoint such a man to a
position that is largely scientific in nature clearly shows
that the ability to consider evidence is not a valued attribute. In the UK, the fact that David Tredinnick MP, a supporter of astrology and homeopathy, is allowed to sit on
the Commons Health Committee,7 gives a similar vibe.
It is in this context that the work of MPs such as Cambridge’s Julian Huppert become even more important.
As the only former research scientist in the Commons,
Huppert is best acquainted with the scientific method—
not only its benefits, but, crucially, its limitations. It is
no surprise that Julian has been a key part of the Lib
CAMBRIDGE
Governments must do
what is best for everyone.
Evidence is the best way
to achieve this
Dems’ move towards an evidence-based drugs policy.
The advocacy of Huppert and MPs of similar disposition
is vital to ensure that the government can move towards
the right balance.
No-one is advocating technocracy. The situation is far
better than it has been in the past. Yet, despite science’s
increasingly high profile in the world, governments
have yet to strike the right balance. They need to go further to give evidence its rightful place in policymaking.
The sooner they do, the sooner they can be said to be
truly serving their people.
references
1. Tran, M. (2009). Government drug adviser David Nutt sacked. The Guardian.
[online] Available at: http://www.theguardian.com/politics/2009/oct/30/drugs-adviser-david-nutt-sacked [Accessed 27 Dec. 2014].
2. Hayek, F. (2014). Friedrich August von Hayek - Prize Lecture: The Pretence of
Knowledge. [online] Nobelprize.org. Available at: http://www.nobelprize.org/
nobel_prizes/economic-sciences/laureates/1974/hayek-lecture.html [Accessed 27
Dec. 2014].
3. Dustmann, C. and Frattini, T. (2014). The Fiscal Effects of Immigration to the
UK. Econ J, 124(580), pp.F593-F643.
4. The Japan Times, (2014). Sweden can’t avoid debate on immigration, analysts
say | The Japan Times. [online] Available at: http://www.japantimes.co.jp/
news/2014/12/28/world/social-issues-world/sweden-cant-avoid-debate-on-immigration-analysts-say/#.VKlUCSusWGo [Accessed 4 Jan. 2015].
5. Australian Government Productivity Commission 2010, Strengthening Evidence
Based Policy in the Australian Federation, Volume 2,Chapter 1, Roundtable
Proceedings, Productivity Commission, Canberra.
6. Goldenberg, S. (2014). Climate change denier Jim Inhofe in line for Senate’s top
environmental job. The Guardian. [online] Available at: http://www.theguardian.
com/environment/2014/nov/06/climate-denier-jim-inhofe-in-line-for-senates-topenvironmental-job [Accessed 27 Dec. 2014].
7. BBC News, (2014). Astrology can aid healthcare - MP. [online] Available at: http://
www.bbc.co.uk/news/uk-politics-28464009 [Accessed 27 Dec. 2014].
8. http://commons.wikimedia.org/wiki/File:International_law_books_(8147928376).
jpg
9. Photo by DAVID ILIFF. License: CC-BY-SA 3.0
7
CAMBRIDGE
Jane P
epigene
lamarckian
Jane is a first year studying
Natural Sciences at Peterhouse.
Often found in deep trance
simulating intelligent activity
or scouring the streets of
Cambridge for things that
catches her fancy.
8
CAMBRIDGE
Phea
etics &
inheritance
an underlying paradox of the Darwinian theory of evolution is that while living organisms are
constantly adapting to the environment, these adaptations are not passed on to the DNA in the reproductive cells and are consequently not inherited. 
Rather, random mutations seem to be fixed by natural
selection (biased selection of mutations based on the
benefits it confers to an organism in a particular environment) or by genetic drift (random fluctuations
in frequencies of mutations that results in them being either fixed or diminished in a population). Lamarck’s “use and disuse” theory may be a solution to
this paradox, but there remains parts of his theory
that lack satisfactory explanation.
9
CAMBRIDGE
In Lamarck’s theory, body parts that are in constant
use will be strengthened, while those unused will be diminished.  A classic example is that of a giraffe’s neck.
It is postulated that the predecessor of the giraffe had
somewhat short necks, and that the muscles in their
necks were strengthened and lengthened by persistent
stretching to reach leaves on high trees. This lengthening was subsequently inherited through the generations, each having slightly longer necks, gradually yielding the organism we now call a giraffe. It is unlikely that
the strengthening of muscles (adaptation) will result in
corresponding changes to the DNA (inheritance), and
therefore this is a gap in his theory.
Epigenetics appears to be the ‘missing link’ connecting adaptation and inheritance that bridges the gap in
Lamarck’s theory, akin to the modern synthesis that
unifies genotype (the sum total of genes present in an
organism) and phenotype (observable traits of an organism). In this article, I shall attempt to address the plausibility of epigenetics as a mechanism of adaptation and
the controversies surrounding it.
ence in morphology between the queen bee and worker
bee, dependent solely on whether a bee was fed royal
jelly during its developmental phases. These differences arise despite the fact that both the worker bee and
queen bee share identical DNA sequences2.3 Another example would be the divergence of mammalian cells from
the initial zygote to form such hereditawry cell lineages
as the nerve cells and muscle cells. After differentiating in the early stages of development, nerve cells will
only give rise to nerve cells and muscle cells to muscle
cells, and cells would not generally revert to other cell
types.4 These phenotypic differences arise due to the
modulation of gene expression patterns (the activation
or repression of certain genes) by the epigenetic factors
without changing the underlying DNA sequence.
Such is epigenetics. The current interest lies in the
mechanisms by which the environment may cause these
changes, and subsequently, whether these changes may
transcend both the organismal and cellular level and
persist through several generations, the importance of
which cannot be comprehended fully without a brief understanding of inheritance.
Epigenetics appears to
be the missing link…
that bridges the gap in
Lamarck’s theory
epigenetics
The definition of epigenetics that shall be adopted in
this article is the study of modifications to the DNA that
are heritable and does not change the underlying DNA
sequence. These modifications consequently contribute
to a perpetuation of altered states (phenotypes) in an
organism.1
The types of modifications that constitute epigenetics
are numerous, but the most closely studied ones are1
DNA methylation, which involves the addition of methyl
groups to regions of DNA and2 modifications of histone
proteins (proteins around which DNA is wrapped to facilitate the formation of a compact chromatin structure),
which entails the addition of certain groups, e.g. methyl,
phosphate and acetyl. As both these modifications involve DNA, it may be that changes in these modifications would subsequently be passed on to an organism’s
offspring via the nucleus of reproductive cells, though
this remains the subject of much controversy.
There are some striking examples of phenotypic variability which are thought to be due to underlying epigenetic rather than genetic differences. One of the most
powerful examples of epigenetics is that of the differ-
10
Jean Baptiste Lamarck
lamarckian inheritance:
a valid proposal? 
The generally accepted mode of inheritance is that akin
to August Weismann’s proposal, which consists of a few
main thrusts:
1.
2.
3.
The soma (all cells in the body except the egg and sperm
cells) and germ-plasm (egg and sperm cells) are disparate.
Changes, if any, acquired through the lifetime of an individual due to such factors as stress or changes in the environment, accumulate in the soma, not in the germplasm.
These changes are not passed on to the offspring.
CAMBRIDGE
REPRODUCED FROM [11]
Therefore, the Lamarckian idea of “use and disuse”
is duly discredited, as (according to this theory) the
environment has no means of inducing changes in the
germ cells.5 Currently, developments in epigenetics has
prompted a resurgence in interest in the inheritance of
acquired characteristics as a valid mechanism for evolution, as epigenetics could be a means of mediating
heritable changes induced by the environment. These
changes must affect the germ-plasm, and subsequently
be transferred along with the germ cell during fertilization in order to effect changes.
experimental evidence for
transgenerational inheritance
A recent experiment published in Nature Neuroscience
seems particularly promising.6 Male mice (F0) were conditioned to associate fear with the smell of acetophenone
by being administered a mild foot shock when exposed
to the smell. These conditioned mice were more prone
to shuddering when exposed to loud sounds when compared to normal mice and this sensitivity was passed on
to first (F1) and second generation (F2) offspring. Remarkably, F0, F1 and F2 mice have lower methylation
levels in the gene (in the sperm) that codes for the acetophenone receptor, which translates to higher sensitivity to that particular odour. Lower methylation levels
often correlate with increased gene expression.
This experiment is noteworthy for the precautions
taken to eliminate certain confounding factors.1 The
mice were conditioned with two different odours (acetophenone and propanol), yielding near identical results.2 A maze test was carried out, and the offspring
of conditioned mice responded as per normal mice,
which rules out the possibility that they were simply
more anxious in general.3 Some mice were conceived
using IVF to prevent transmission of odor sensitivity due to interactions between the father and mother
mice.4 Cross-fostering of mice (offspring of conditioned
mothers were fostered by non-conditioned mothers and
vice-versa) were carried out to eliminate maternal effects.5 Methylation levels were screened in two different genes, one coding for the acetophenone-detecting
receptor and another that codes for a receptor detecting
a separate odour, and it was found that only the former showed statistically significant differences in DNA
methylation levels.
In two separate stress-related experiments on mice,
alterations in DNA methylation were found to correlate
with1 stress levels experienced by the father and2 attention received from the mother.78 In the former experiment, offspring of stressed mice had a higher susceptibility to depression-like states while in the latter
experiment, mice who received more attention from
their mothers were shown to cope better under stress.
Meanwhile, Agouti variable yellow female mice who had
varying amounts of methyl supplements in their diets
during gestation had offspring with differing colour
coats and susceptibility to obesity, the effects of which
is also attributed to DNA methylation.
For all these experiments mentioned above, it is postulated that induced changes in the environment would
result in changes in methylation patterns on DNA in
mice, which are subsequently passed through the generations. This supports the notion that epigenetics may
indeed facilitate the inheritance of acquired characteristics. But for complete acceptance of this theory, some
hurdles remain to be overcome.
11
CAMBRIDGE
limitations and uncertainties
1.
2.
3.
How exactly does the environment posit these changes?
Do receptor molecules, in the case of the odour experiment, interact with and somehow activate proteins that
methylate or de-methylate DNA?
Given that the environment is able to induce changes in
the methylation status of DNA, how are these modifications passed on to the offspring? During the process of
gamete synthesis and post-fertilization, most DNA modifications are removed, resulting in a blank state of sorts.
Changes can only be propagated if the modifications escape this process or if modifications were made directly
to the reproductive cells.
A limitation of the Nature Neuroscience study is that it
was confined to the settings of an experimental laboratory. Thus, any changes in the epigenetic status of the DNA
would have been artificially induced, and it is hard to argue that nature would disrupt DNA in a similar manner,
or that “mutations” of this kind will have a discernible
effect on inheritance.
4.
Another question to note is whether these modifications
persist long enough to be transmitted through the generations? Are the effects sufficient to posit long-term evolutionary change or do they simply act as short-term adaptations that are muffled and counterbalanced over the
course of time? 
All in all, it may be surmised that epigenetics may
be a plausible channel to propagate Lamarckian inheritance, and that there is a plethora of experimental evidence in plants and worms to support this school of
thought, though similar evidence in mammals are fewer
and far-between.  A dose of skepticism is still warranted
in the face of intricacies surrounding this new field,  but
“the inheritance of differential epigenetic information”
that “could potentially contribute to altered traits or disease susceptibility in offspring and future descendants”
“has a deliciously Lamarckian flavour… difficult to resist.”1,20
references
1. Bird, A. Perceptions of epigenetics Nature 2007;447 : 396-398 http://www.nature.
com/nature/journal/v447/n7143/full/nature05913.html?message=remove&lang=en
(Accessed 24 December 2014)
2. Kucharski R, Maleszka J, Foret S, Maleszka R. Nutritional Control of Reproductive
Status in Honeybees via DNA Methylation. Science 2008; 319 (5871) : 1827-1830.
http://www.sciencemag.org/content/319/5871/1827.full (Accessed 24 December 2014)
3. Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV,
Feinberg AP. Reversible switching between epigenetic states in honeybee behavioral
subcastes. Nature Neuroscience. 2012. 15: 1371–1373. http://www.nature.com/neuro/
journal/v15/n10/full/nn.3218.html (Accessed 24 December 2014)
4. Jablonka E, Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and
Implications for the Study of Heredity and Evolution. The Quarterly Review of
Biology. 2009; 84(2) : 131-176. http://www.jstor.org/stable/10.1086/598822 (Accessed
24 December 2014)
5. Weismann A, The germ plasm : a theory of heredity. Trans Parker WN, Rönnfeldt H.
New York: Charles Scribner’s Sons; 1893. p 463
6. Dias BG, Ressler KJ. Parental olfactory experience influences behavior and neural
structure in subsequent generations. Nature Neuroscience. 2014;17 : 89-96
http://www.nature.com/neuro/journal/v17/n1/abs/nn.3594.html (Accessed 24 Dec
12
2014)
7. Dietz DM, LaPlant Q, Watts EL, Hodes GE, Russo SJ, Feng J, Oosting RS, Vialou V,
Nestler EJ. Paternal Transmission of Stress-Induced Pathologies. Biol Psychiatry.2011;
70(5): 408–414. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217197/ (Accessed 24
December 2014)
8. Chen Z, Riggs AD. DNA Methylation and Demethylation in Mammals. J. Biol. Chem.
2011, 286:18347-18353 http://www.jbc.org/content/286/21/18347.long (Accessed 24
December 2014)
9. Schmitz RJ, The Secret Garden—Epigenetic Alleles Underlie Complex Traits. Science
2014;343 (6175):1082-1083. http://www.sciencemag.org/content/343/6175/1082.full
(Accessed 24 December 2014)
10. University of Cambridge. Scientists discover how epigenetic information could be
inherited. http://www.cam.ac.uk/research/news/scientists-discover-how-epigenetic-information-could-be-inherited (Accessed 24 December 2014)
11. ttp://cnx.org/contents/41c4c77e-a44c-431f-bbc032eb72726630@1/Basic_Principles_of_Genetics
12. http://commons.wikimedia.org/wiki/File:Lab_mouse_mg_3216.jpg
CAMBRIDGE
Hugh Wilson is studying Part III
Physics at Downing College. He is
especially interested in Biophysics
and Biotechnology.
synthetic biology:
the next revolution?
hugh wilson
13
H
CAMBRIDGE
umans may not be the only
tool users, but more than any other life we have augmented our powers beyond the base established by nature. Early efforts in any new technology rely on trial
and error guided by intuition. As our understanding improves, the guiding principle changes from trial and error to predictive design. However, the technology does
not truly affect people until we capture our ability to
manipulate the world in predictable devices (think of
electrical circuits as devices which manipulate electromagnetic fields). The importance of this step is that one
set of engineers can make the devices, while another can
ignore how the devices work, but combine them into
systems which solve problems. The technological revolutions which have shaped human history rest on this
principle of dividing work between specialised groups.
In the 18th Century, there was a revolution in transforming energy: the Industrial Revolution. In the 20th
Century, there was a revolution in information processing: the advent of widespread computing. In the 21st
Century, Synthetic Biology is poised to revolutionise
our ability to manipulate matter. The current bespoke efforts of biotechnology will be replaced by a paradigm in
which predictable biological components are combined
to create devices. The process will shadow the construction of electronic devices from electrical components
and the power of biology will become accessible to all.
At least, this is the view of proponents of the field. The
truth is much less certain.
After long theoretical discussion, Synthetic Biology
came into existence as a practical discipline near the
turn of the millennium when the first synthetic genetic
devices were demonstrated in live cells. In a short time,
the field has garnered a huge amount of interest. The
media attention has been intense;1,2 DARPA has declared
that rapid engineering of biological systems is one of
the highest national priorities;3 and a presidential commission was formed to report on how America can reap
“the benefits of this developing field of science while
identifying appropriate ethical boundaries and minimising identified risks”.4
The reason for this attention is that Synthetic Biology
makes big promises. We will harness microbes to produce biofuel;5 engineer more efficient photosynthetic
plants to meet the global energy shortage;6 and perhaps
even make ourselves immune to viruses.7 A more sober
14
inspection of the field reveals that many of these claims
are hopes for the future. However, there has been real
progress towards solving significant problems. A good
example is the construction of a toggle switch in E. coli
by Collins et al.8 The bacterium they produced could
be switched from expressing one gene to another using chemical and thermal stimuli. A second example is
the work of Jay Keasling.9 He and his team have genetically engineered yeast to artificially produce a potent
anti-malarial, artemisinin. The new synthetic source is
more stable and cheaper than existing sources, which
means the work will significantly improve the lives of
many people.
Yet doubt still hangs over Synthetic Biology: to solve
global problems we need a library of predictable and
interchangeable components to rival that of electronics.
This library would be a significant milestone in the development of Synthetic Biology, but progress towards
it has been mixed. A large number of components have
been generated, but many are poorly described and fail
to work when removed from their original organism
and system. Will we ever reach the goal? It is difficult to
be certain; the success of Synthetic Biology will hinge
on our progress against technical hurdles and on the
attitude and policies we adopt as a society.
Synthetic Biology is
poised to revolutionise
our ability to manipulate
matter
The technical problems can be broken into four main
areas.10 Firstly, many of the components are not well
characterised: for example, certain components code
for the creation of coloured proteins, but it is unclear
exactly how the absorption spectrum of the cell will be
affected. This lack of information is a problem. We must
know how a component behaves before we can include
it in the design of a complex system. Secondly, even
with well-characterised components, the behaviour of a
system can differ from what we would predict. Thirdly,
even when a component works exactly as expected it
can have an adverse, even fatal, effect on the viability of
the host. Finally, random fluctuations within the cell can
mean the behaviour of a system is not consistent over
time. These four technical problems lead to a question:
is the apparent modularity of nature a genuine property or is it an artefact of how humans try to understand it? To answer this question scientists are attempting to build lifelike systems which are less extensively
interlinked and so more amenable to the goal of packaging biological function into devices.
In 2005 Drew Endy altered the bacteriophage (virus)
T7 by rewriting its genome to reduce the interaction
between different genes.11 The altered bacteriophage
maintained the key features of the original, but was
easier to understand, model and manipulate. Now an international consortium is doing the same for the whole
yeast genome12 and they have already published one
chromosome.13 This field of research is often termed
“synthetic genomics” and an important practical goal is
to develop generic platforms for biotechnology.
It is not only technical hurdles which face Synthetic
Biology. People hold strong views about whether it is
morally acceptable to manipulate life. Synthetic genomics is subject to claims that scientists are trying to play
God.14 Additional concerns are centred around the problem of “dual-use”: Synthetic Biology lays the foundation
for bioterrorism as well as for a host of beneficial applications. In 2002 Professor Eckard Wimmer was able
to synthesise poliovirus from scratch from the publicly
available viral sequence and mail-order pieces of DNA.15
As with any new technology the potential benefits of
Synthetic Biology are accompanied by risks. However,
safety controls, such as a switch to kill modified organisms, can be used to push the balance of opinion towards continued development.
There is an additional problem of perception. GM
technology is partly unpopular because it is seen as a
mechanism by which control is transferred from individuals to unaccountable trans-national corporations.
This sentiment is evident in the animosity directed at
agribusiness companies such as Monsanto.16 The same
fears should not be applied to Synthetic Biology, which
is fundamentally a force for the democratisation of science and technology. An annual demonstration of this
fact is present in the form of the iGEM (international
Genetically Engineered Machine) competition, which
invites school, undergraduate and postgraduate teams
from around the world to develop new applications of
CAMBRIDGE
Synthetic Biology and share them openly at a global
meeting.17
The further impact of society on Synthetic Biology
comes in how we deal with the issues of ownership and
intellectual property. The mixed parentage of the field
manifests itself in the range of solutions offered to this
problem. Ideas from engineering and software development have led to the BioBricks Foundation with the
mission statement: “to ensure that the engineering of
biology is conducted in an open and ethical manner to
benefit all people and the planet”.18 On the other side,
bio-tech organisations, such as the Venter Institute, believe that a proprietary climate is necessary. They argue
patents are required to encourage investors to support
vital foundational research. However, it is certainly possible for overly broad patents to stymie new technology. For example, zinc finger nucleases were a promising
technology that allows segments of DNA to be inserted
at a specific site in the genome. The Californian company Sangamo Biosciences holds a comprehensive patent
for the technology and many believe progress with the
tool has been slow as a result.19
It seems Synthetic Biology is a field which has promised much and not yet completely delivered. Whether
it will ultimately be able to fulfil its promises depends
equally on our progress against technical hurdles and
on how as a society we choose to interact with the possibilities it presents.
references
1. Michael Specter; “A life of its own: where will synthetic biology lead us?”; The New
Yorker 2009; September 28
2. W. Wayt Gibbs; “Synthetic Life”; Scientific American; May 2004
3. DARPA (Defense Advanced Research Projects Agency) http://www.darpa.mil/
our_work/
4. Presidential Commission for the Study of Bioethical Issues; “NEW DIRECTIONS:
The Ethics of Synthetic Biology and Emerging Technologies”; December 2010;
available from: http://bioethics.gov/sites/default/files/PCSBI-Synthetic-Biology-Report-12.16.10_0.pdf
5. Michael S Ferry, Jeff Hasty, Natalie A Cookson; “Synthetic biology approaches to
biofuel production”; Biofuels (2012); 3(1), 9-12
6. Biotechnology and Biological Sciences Research Council; “Human-made photosynthesis to revolutionise food and energy production” February 17, 2012; available at:
http://www.sciencedaily.com/releases/2012/02/120217145755.htm
7. George Church, Ed Regis; “Regenesis: How Synthetic Biology Will Reinvent Nature
and Ourselves” ISBN-10: 0465021751; ISBN-13: 978-0465021758
8. Timothy S. Gardner, Charles R. Cantor, James J. Collins; “Construction of a genetic
toggle switch in Escherichia coli”; Nature (2000); 403: 339-342
9. C. J. Paddon et al.; “High-level semi-synthetic production of the potent antimalarial
artemisinin”; Nature (2013); 496; 528-532
10. Roberta Kwok; “Five Hard Truths For Synthetic Biology”; Nature (2010); 463: 288-290
11. Leon Y. Chan, Sriram Kosuri, Drew Endy; “Refactoring bacteriophage T7”; Mol Syst
Biol (2005)
12. Synthetic Yeast 2.0: Building the world’s first synthetic eukaryotic genome together;
http://syntheticyeast.org/
13. Annaluru et al.; “Total Synthesis of a Functional Designer Eukaryotic Chromosome”;
Science (2014); vol. 344; pp. 55-58; published online: http://www.sciencemag.org/
content/344/6179/55.abstract
14. Fiona Macrae; “Scientist accused of playing God after creating artificial life by making designer microbe from scratch – but could it wipe out humanity?”; Mail Online
June 2010; available at: http://www.dailymail.co.uk/sciencetech/article-1279988/Artificial-life-created-Craig-Venter--wipe-humanity.html
15. Eckard Wimmer; “The test-tube synthesis of a chemical called poliovirus: The simple
synthesis of a virus has far reaching societel implications”; EMBO Rep. (2006) 7:
S3-S9
16. Lessley Anderson: “Why Does Everyone Hate Monsanto?”; http://modernfarmer.
com/2014/03/monsantos-good-bad-pr-problem/
17. The International Genetically Engineered Machine (iGEM) Foundation: Synthetic
Biology based on standard parts; http://igem.org/About
18. BioBricks Foundation: Biotechnology in the public interest; http://biobricks.org/
19. Thomas Scott; “The zinc finger nuclease monopoly”; Nature Biotechnology (2005);
23: 915-918
15
CAMBRIDGE
Understanding the Immune System—
A potential cure for cancer?
Wearn Xin Yee
Wearn Xin is currently a first year Natural
Sciences (Biological) student at Trinity
Hall who likes reading about pathogenic things and working in the lab. She
decided to write on this topic when she
discovered a side of the immune system
she wasn’t aware of before.
16
C
ancer is one of the leading causes
of death in industrialised nations and is caused by the
progressive growth of the progeny of one transformed
cell. One way in which the body protects itself is through
the immune system. In a healthy human body, the immune system is able to recognise potentially cancerous
cells and destroy them before they invade the tissues.1
CAMBRIDGE
MHC class 1 molecules and can no longer be recognised
by cytotoxic T cells, it might still be susceptible to NK
cells.3
However, cancer cells are also able to evade the immune system. For one, tumours seem to be able to evade
immune attack by creating a generally immunosuppressive environment. They may secrete immunosuppressive cytokines such as TGF-beta that suppresses inflammatory T-cell responses and cell-mediated immunity
necessary for tumour cell control. Also, tumour cells
can secrete molecules such as collagen and mucin to
create a physical barrier to the immune system, thus
preventing their detection and destruction,3,4 These
mechanisms allow tumours to avoid immune recognition and continue to grow in the body.
immune system and cancer
immunotherapy—how the immune system may ‘cure’ cancer
Tumour cells are usually recognised by cells of the adaptive immune system such as CD4 helper T cells, CD8
T cells, and natural killer (NK) cells. Upon recognition,
CD8 and NK cells kill cells by releasing cytotoxic granules, whilst CD4 helper T cells activate other cells of
the immune system to kill the target cells. IFN-gamma
(secreted by NK and CD8 cells) and IFN-alpha are important in the elimination of tumour cells, either directly or indirectly through actions on other cells. Another
important player in cancer is the Treg cells, which can
hamper anti-tumour immune response and thus influence the body’s reaction to cancerous cells.2
One example of the immune system in action is that
when cells mutate, these cellular transformations are
frequently associated with the expression of MHC class
1b proteins (such as MIC-A and MIC-B) on the cell surface. NK cells recognize and kill the cells. The variety of
ways that the immune system can kill cancerous cells
means that there are several ‘safety nets’ in place: for
example, even when a tumour loses expression of all
As the search for a cure to cancer continues, some scientists are turning to modifying what the human body
already has for a safe and efficient cure. Considering
that a healthy immune system can recognise cancerous
cells, one target for modification and exploitation is the
immune system — indeed, immunotherapy research involves the exploitation of components of the immune
system to attempt to cure cancer.
One such ‘drug’ involving components in the immune
system is IFN-alpha. Belonging to the interferon family,
one of its roles is to activate NK cells to increase their
cytotoxic activity.5 Currently, it is the only interferon
approved by FDA to treat certain cancers such as kidney
cancer, and melanoma; other IFNs are currently under
research. As a form of therapy, it has been shown to
slow the growth of cancer and blood vessels supporting
tumour growth and to boost the ability of cytotoxic immune cells to attack cancer cells.6 However, IFN-alpha
must be administered with caution as it demonstrates
high levels of toxicity: during a trial, 67% of patients on
Figure 1: Examples of immune responses against tumour cells (role of IFN alpha not shown). [A]
17
CAMBRIDGE
Figure 2: An example of genetically modified T-cell
research on ovarian cancer. [B]
IFN-alpha2b adjuvant therapy presented Grade 3 toxicities.7
Another area that has shown success is in using
monoclonal antibodies for treatment. This form of treatment involves using these antibodies to bind to proteins
expressed by cancerous cells, thereby flagging them out
for detection and destruction by components of the immune system. This field is certainly promising, as drugs
such as Alemtuzumab (MabCampath) treating chronic
lymphocytic leukaemia (CLL) are already in the market.8 Alemtuzumab binds to the CD52 protein, forming
a complex that favours the deposition of activated complement molecules and facilitates the necessary contacts
for cell mediated killing.9 The preferential targeting of
CLL cells is hypothesised to be due to different membrane proteins associated with CD52 on CLL but not on
T cells.10 However, major disadvantages to monoclonal
antibodies are that their large size prevent easy penetration of tumours, and that it may be expensive to mass
produce as the complexity of the active antibodies require sophisticated eukaryotic machinery to produce.11
Genetically modifying cells involved in the immune
system is another approach scientists are trying; specifically, scientists have worked to engineer T cells to target
cancerous cells. In one experiment targeting leukaemia,
T cells from the peripheral blood were isolated and reprogrammed into induced pluripotent stem cells before
being transfected with a gene coding for a receptor for
antigen CD19 using disarmed retroviruses. Upon redifferentiation into T cells, they are injected back into the
patient, whereby they can track down and kill cells presenting CD19 (i.e. both cancerous and normal B cells),12
and research is being done to improve specificity to cancerous B cells only13 Such a therapy shows promise as
a study showed that the conditions of all 13 multiple
myeloma patients treated with genetically engineered T
cells that can recognise proteins found on tumour cells
but not on healthy cells (such as NY-ESO-1) improved.14
18
Figure 3: Development of cancer vaccine [C]
Unfortunately, there may be adverse effects in this
approach due to on-target but off-tumour effects. These
may be as serious as causing cardiac death, as was the
case in a trial when mutations to the alpha chain of the
T cell receptor aimed to enhance affinity to tumour cells
recognised and targeted other peptides found in cardiomyocytes instead.15
‘Vaccine’ for cancer? Indeed, researchers are aiming
to do so using dendritic cell lines by firstly removing
monocytes from the patient and differentiating in vitro
into dendritic cells. Dendritic cells are then exposed to
cancer cells or antigens to ‘prime’ them before they are
proliferated. These dendritic cells are then injected back
in to the body, where they in turn prime T cells to recognise the tumour-specific antigen, thus mounting an
immune response to cancerous cells,16,17 However, its
success is limited as some cancer cells no longer express cancer cell specific molecules, thus reduction in
tumour load has not been frequently observed.18
Lastly, another promising approach to cancer therapy is the blocking of immune checkpoints. Immune
Figure 4: Ipilimumab mechanism of action [D]
checkpoints control signals involved in self-tolerance
and T-cell responses, and many tumours use this to be
resistant to the immune system. To block these checkpoints, ligand-receptor interactions at these checkpoints
are interfered such as by antibodies. Currently, there are
three immune checkpoint inhibitors in the market, the
earliest being ipilimumab, which had a large impact on
metastatic malignant melanoma treatment,19,20 It works
by blocking an important negative regulator of the antitumor T-cell response, eventually allows for increasing
T-cell activation which can then seek out tumours.21
However, there are side effects too as by blocking
immune checkpoint inhibitors, autoimmune side effects
may occur, ranging from rash to endocrinopathies.22
Overall, there are several methods in immunotherapy, not limited to those discussed here, currently being
developed. Many of these processes are complex, mainly because many mutations in the cancerous cell allow
it to escape detection. Moreover, antigens presenting on
tumour cells may be similar to proteins presenting on
normal cells. Taken together, it becomes extremely difficult to find a single cure that cures all cancer effectively without any dangerous side effects. Yet, as research
continues, current cancer treatments and survival rates
may hopefully improve.
CAMBRIDGE
scientists are looking to combining different drugs and
different therapies with immunotherapy for better treatment. The understanding of immunotherapy has even
led some researchers to believe that successful chemotherapy and radiation treatment may be partly due to
the release of antigens through these therapy that the
immune system can respond to—a form of natural ‘immunotherapy’.23 Whilst much research still needs to be
done before immunotherapy can be officially introduced
as a form of cancer treatment, it is certainly an area of
large potential.
the future of immunotherapy
Immunotherapy certain holds a bright future—in 2013,
cancer immunotherapy was named the breakthrough of
the year by the Science magazine. As immunotherapy
offers a more targeted approach to cancer treatment,
references
1. ‘Huge breakthrough’ in understanding how the immune system recognises cancer.
(2014, November 21). Retrieved January 23, 2015, from http://www.cancerresearchuk.
org/about-us/cancer-news/news-report/2014-11-21-huge-breakthrough-in-understanding-how-the-immune-system-recognises-cancer
2. Acton, Q. (2012) Cancer: New Insights for the Healthcare Professional: 2011 Edition.
ScholarlyEditions
3. Murphy, K. (2012). Janeway’s immunobiology (8th ed.). New York: Garland Science.
4. Kufe, D.W. (2010).Mucins in cancer: function, prognosis and therapy. Nature Reviews
Cancer, 9(12), 874-885
5. Jewett, A. , & Bonavida, B. (1995). Interferon-alpha activates cytotoxic function but
inhibits interleukin-2-mediated proliferation and tumour necrosis factor-alpha
secretion by immature human natural killer cells. Journal Clinical Immunology, 15(1),
35-44.
6. Non-specific cancer immunotherapies and adjuvants. (n.d.). Retrieved December 27,
2014, from http://www.cancer.org/treatment/treatmentsandsideeffects/treatmenttypes/immunotherapy/cancer-immunotherapy-nonspecific-immunotherapies
7. Sabel, M. and Sondak, V. (2003) Pros and cons of adjuvant interferon in the treatment
of melanoma. The Oncologist, 8(5), 451-458.
8. About monoclonal antibodies. (n.d.). Retrieved December 27, 2014, from http://www.
cancerresearchuk.org/about-cancer/cancers-in-general/treatment/biological/types/
about-monoclonal-antibodies
9. Alinari, L., Lapalombella, R., Andritsos, L., Baiocchi, R.A., Lin, T.S. and Byrd, J.C.
(2007). Alemtuzumab (Campath-1H) in the treatment of chronic lymphocytic leukaemia. Oncogene, 26, 3644-3653.
10. Mone, A.P., Cheney, C., Banks, A.L., Tridandapani, S., Mehter, N., Guster, S., Lin, T.,
Eisenbeis, C. F., Young, D.C. and Byrd, J.C. (2006) Alemtuzumab induces caspase-independent cell death in human chronic lymphocytic leukaemia cells through a lipid
raft-dependent mechanism. Leukaemia, 20, 272-279.
11. Chames, P., Van Regenmortel, M., Weiss, E. and Baty, D. (2009) Therapeutic antibodies:
successes, limitations and hopes for the future. British Journal of Pharmacology,
157(2), 220-233
12. Palmer, C. (2013, August 11). Tumour-Targeting T Cells Engineered. The Scientist.
13. Kershaw, M., Westwood, J., Slaney, C. and Darcy, P. (2014). Clinical application of
genetically modified T cells in cancer therapy. Clinical and Translational Immunology,
3(16).
14. Coghlan, A. (2012, December 11). Souped-up immune cells force leukaemia into
remission. New Scientist.
15. Heslop, H.E. (2013) Genetic engineering of T-cell receptors: TCR takes to titin. Blood,
122(6), 853-854.
16. Laborde, R.R., Lin, Yi., Gustafson, M.P., Bulur, P.A. and Dietz, A.B. (2014) Cancer
vaccines in the world of immune suppressive monocytes (CD14+HLA-DR(lo/neg)
cells): the gateway to improved responses. Frontiers in Immunology. doi: 10.3389/
fimmu.2014.00147
17. Dendritic Cell Therapy. (n.d.). Retrieved January 5, 2015, from http://cancer.stanford.
edu/research/immunology/dendritic.html
18. Bodey, B., Bodey, B. Jr, Siegel, S and Kaiser, H. (2000) Failure of cancer vaccines: the
significant limitations to this approach to immunotherapy. Anticancer Research,
20(4): 2665-2676.
19. Pardoll,D. (2012). The blockade of immune checkpoints in cancer immunotherapy.
Nature Reviews Cancer, 12: 252-264
20. Webster, R. (2014). The immune checkpoint inhibitors: where are we now? Nature
Reviews Drug Discovery, 13: 883-884
21. Tarhini, A., Lo, E. and Minor, D. (2010). Releasing the brake on the immune system:
ipilimumab in melanoma and other tumours. Cancer Biotherapy and Radiopharmaceuticals, 25(6): 601-613
22. Corsello, S., Barnabei, A., Marchetti, P., De Vecchis, L., Salvatori, R. and Torino, F.
(2013) Endocrine side effects induced by immune checkpoint inhibitors. Journal of
Clinical Endocrinology Metabolism, 98(4): 1361-1375
23. Cancer Immunotherapy: The Next Decade? (n.d.). Retrieved December 27, 2014, from
http://www.cancerresearch.org/news-publications/our-blog/january-2014/cancer-immunotherapy-the-next-decade
Images
[A] (Figure 1): Gilboa, E. (2004) The promise of cancer vaccines. Nature Reviews
Cancer, 4, 401-411
[B] (Figure 2): Department of Obstetrics & Gynecology. (n.d.). Retrieved January 6,
2015, from http://www.uphs.upenn.edu/obgyn/research/ovarian_clinical.htm
[C] {Figure 3}: Cancer Vaccines, CSA - Discovery Guides. (n.d.). Retrieved January 6,
2015, from http://www.csa.com/discoveryguides/cancer/review.php
[D] (Figure 4): Weber, J. (n.d.). Anti-CTLA-4 Monoclonal Antibodies for the Treatment
of Malignant Melanoma. Retrieved January 23, 2015, from http://www.medscape.org/
viewarticle/584180
19
JOHNS HOPKINS
Implications of
Synthetic Life
Sohail Zahid
in the past decade, scientists have made discoveries
that challenge the foundation of commonly held beliefs.
From the reclassification of Pluto to a dwarf planet in
20051 to the discovery that the moon contains significant reservoirs of water in 20092 and the assertion that
gravity is simply a macroscopic phenomenon of entropic movement in 2010,3 the common perceptions of scientific truth become readjusted year after year.
The notion of life itself became challenged when
Craig Venter announced that researchers in his institution had successfully constructed the first instance of a
replicating, synthetic organism. The research team of 46
scientists first built a comprehensive, synthetic genomic
database of the bacterium, M. mycoides, which they assembled in yeast cells in DNA cassettes of approximately 1,000 base pairs each.4 Afterwards, the genome of M.
capricolum was hallowed out and the synthetically created genome was transplanted from yeast to these target
bacterium cells. The result, after 15 years and $40 million dollars in investment, was M. mycoides JCVI-syn1.0,
an organism with synthetic origins from a computer.
It is important to note that the Venter group did not
write a new bacterium genome from scratch, but instead
reengineered and modified a preexisting genome of M.
myocoides. Hence, there is still controversy in the scientific community as to whether or not this achievement
20
Sohail Zahid studies Biomedical Engineering and Applied Math at
Johns Hopkins University.
constitutes synthetic life. Still, this feat in synthetic biological construction is unprecedented since a biological
structure of this magnitude had never been created before;4 most chemical synthesis techniques stop working
after the transcription of one thousand base pairs. To
expand to the full genome of one million, the research
team stitched together custom made DNA cassettes, specifically designed to bind to an adjacent genetic fragment. In a painstaking effort, scientists had to make sure
each base pair in the multi-million sized genome was
perfectly arranged since a single inaccuracy could have
prevented the DNA cassettes from assembling or could
have prevented the bacterium from self-replicating.
However, with advanced DNA sequencing techniques,
the research team was able to complete this daunting
task with minimal error.
Due to the sheer scale of this achievement, the upcoming consequences—which have been overlooked in
the infant stages of synthetic biology—are just now entering the spotlight. Recently, Craig Venter opened up a
company, Synthetic Genomics,5 to act as an innovator in
the production of genomic-driven solutions to contemporary problems.
JOHNS HOPKINS
“Designer viruses” or “Frankenstein bacteria” with significant resistive capabilities may pose a danger more serious
than cancer or HIV today.
This discovery, first and foremost, changes the landscape of basic biomolecular research. Synthetic biology,
whether at the organismal level, chromosomal level, or
even at the DNA level, can redefine the way gene pathways are regulated and how biochemical networks are
assayed.6 Instead of working around possible roadblocks
in biological networks or dealing with unwanted side
effects from a required metabolite, researchers can conceivably custom design molecules to fit their own needs
and specifications. This has unbounded long-term possibilities, as changes at the DNA sequence level can provide new research pathways that may someday produce
vaccines and drugs for today’s more elusive diseases,
including cancer, HIV, heart disease, and autism.
Currently, synthetic biology techniques are being
used in biotechnology companies such as Pfizer, Monsanto, and Merck to design specific medicinal drugs and
agricultural products by manipulating the protein landscape surrounding cells.7 While this discovery opens up
new implications in improving healthcare and improving agricultural production, it also opens up the reality of utilizing synthetic techniques to explore other
commercial avenues such as energy. Synthetic biology
solutions can optimize the conversion of fossil fuels
such as coal and oil to energy with specific, synthetically manufactured biochemical.8 When fossil fuels
become completely depleted, this technology may provide a new, more robust source of biofuel. For example,
lignocellulosic biomass is an abundant and renewable
plant that could become a low cost, accessible resource
for energy production if this plant were to be manufactured synthetically.9 Some algal products have also been
observed to degrade petroleum products.10 Using genetic engineering, society can not only create an efficient,
self-sustaining biologically-derived fuel source, but also
decrease the carbon footprint that centuries of fossil
fuel use has caused. One way this is being accomplished
is through analyzing the underlying gene regulation.6
By identifying key hubs in the genetic network and regulation with a genetic circuit controls system, specific
proteins can be expressed, suppressed, or selectively
promoted to improve function of the organism.
Since synthetic biology has mostly dealt with smallscale solutions, the large-scale nature of this discovery
opens up some serious legal implications. While Craig
Venter’s scientific achievement is certainly commendable, his overwhelming influence in the field is also a
cause for concern. Venter has already applied for patents on more than 300 artificially constructed genes.11
This raises grave concerns in the future as individuals
begin to lay claim to the basic building blocks of life,
which may be problematic if individuals need syntheti-
21
JOHNS HOPKINS
cally derived solutions to combat disease, and companies
are unable to help because of exclusive patent claims to
a single amino acid.12 Similarly, since Venter may be the
only individual with both the financial resources and the
research team to derive these DNA-driven solutions, his
company, Synthetic Genomics, may become a monopoly in the field. The barrier of entry into this specific
synthetic biology market is significantly high as it encompasses both financial and academic concerns, so
new competitors might be discouraged to enter despite
the potential.13 Because this company will be difficult to
break up since it resides with a sole individual, Craig
Venter, at the helm, a scenario may result in which Synthetic Genomics can issue these necessary, life-saving
solutions at ridiculous prices with no one, including the
government, having the ability to do anything about it.
One of the most serious consequences for this type
of discovery is its role in possible bioterrorism activities, which can arise if resources and techniques fall into
the wrong hands. While certain known diseases such as
Variola, Smallpox, and the 1918 influenza virus are in
locked laboratories, synthetic viruses unleashing these
diseases may become a serious war tool in the future.14
If this technology were to become publically accessible
rather than the property of Synthetic Genomics, the
implications are vast and potentially troublesome. Although it is difficult to manufacture a biologically potent
disease now, it may become considerably easier in the
next decade or so as biochemistry research and development improves. Just as colonists spread blankets with
smallpox to eradicate Native Americans, countries may
send pandemic-inducing diseases through planes or mail
to wipe out entire populations.15 “Designer viruses” or
“Frankenstein bacteria” with significant resistive capabilities may pose a danger more serious than cancer or
HIV today.
Venter’s discovery is now the bioethical “Pandora’s
box” of our age. It is difficult to ascertain all the outcomes, but it is also important to realize that both positive and negative scenarios will result. Society already
has engaged in much debate about the ethical considerations in cloning and embryonic stem cell research.
Synthetic biology will certainly join that forum of discussion as scientists become more successful in creating artificial life and unleash both positive and negative
possibilities. What is important now is for public policy
to keep up with the fast rate of scientific discovery. Education about the risks and benefits will become crucial
in galvanizing this technology to create a better future.
Venter’s discovery is now
the bioethical “Pandora’s
box” of our age.
references
1. NASA. Pluto: Overview [internet]. 2012 [cited 2012 Feb 19]. Available from: http://
solarsystem.nasa.gov/planets/profile.cfm?Object=Pluto
2. NASA. Lunar Impact Uncovered More Than Just Moon Water [internet]. 2012 [cited
2012 Feb 19]. Available from: http://science.nasa.gov/science-news/science-at-nasa/2010/21oct_lcross2/.
3. Verlinde, EP. “On the Origin of Gravity and the Laws of Newton”. JHEP. 2011 Apr; (4)
29: 1-26.
4. Gibson DG et al. “Creation of a Bacterial Cell Controlled by a Chemically Synthesized
Genome.” Science. 2010: 52-56.
5. Synthetic Genomics. The Global Challenge: Sustainably meeting the increasing demand for critical sources [internet]. 2012 [cited 2012 Feb 19]. Available from: http://
www.syntheticgenomics.com/.
6. Alon, Uri. “An Introduction to Systems Biology. Design Principles of Biological
Circuits”. Boca Raton: Taylor & Francis Group, LLC, 2007.
7. Smalley, Eric. “Synthetic Biology Gets Down to Business.” Nature Blogs. 2007 March.
8. Schmidt, CW. “Synthetic Biology: Environmental Health Implications of a New Field”.
Environmental Health Perspectives. 2010 March; (118):a118-a123.
9. Kumar P et al. “Methods for Pretreatment of Lignocellulosic Biomass for Efficient
22
Hydrolysis and Biofuel Production”. Journal of American Chemical Society. 2009; (48)
8: 3713-3729.
10. Thomson, EA. Scientists Study Makeup of Oil-Eating Bacteria [internet]. 1992 [cited
2012 Feb 19]. Available from: http://web.mit.edu/newsoffice/1992/bacteria-0401.html.
11. Sample, Ian. Craig Venter creates synthetic life form [internet]. 2010 [cited 2012 Feb
19]. Available from: http://www.guardian.co.uk/science/2010/may/20/craig-ventersynthetic-life-form.
12. Guttman, Amy. New Directions: The Ethics of Synthetic Biology. Washington D.C.
Presidential Commission for the Study of Bioethical Issues; 2010.
13. Geneva. Risk Governance of Synthetic Biology. International Risk Governance
Council; 2009.
14. RA, Tucker and Zilinskas JB. “The Promise and Perils of Synthetic Biology.” The New
Atlantis. 2006: 25-45.
15. Douglas T and Savulescu J. “Synthetic Biology and the ethics of knowledge”. Journal
of Medical Ethics. 2010 Oct. (36) 10: 687-693.
16. http://commons.wikimedia.org/wiki/File:Physcomitrella_growing_on_agar_plates.jpg
JOHNS HOPKINS
Why the World’s Largest
Landfill is in the Ocean
Stephen Jenkins
humans have been using plastic in its modern form
as an all-purpose tool since its invention in 1907. It can
be found in all walks of life, but recent research has
revealed potentially negative consequences on marine
ecosystems from the ubiquitous use of the material. For
instance, a study published in September, 2011 in Environmental Science and Technology discovered that “a
single garment can release 1900 fibers per wash. The
researchers theorized that a large amount of [the] mi-
a striking example of how the actions of man can harm
the environment.
The Great Pacific Garbage Patch first gained attention
in 1997. It has been difficult to determine the Garbage
Patch’s exact size. With the information that is available though, researchers consider the “combined areas
croplastic debris found in marine environments comes
directly from washing clothes.”1 It is amazing that such
a universal activity can potentially be so destructive to
the environment. Unfortunately, this is the reality of
the Great Pacific Garbage Patch. The Garbage Patch is
characterized by a high concentration of plastic debris
that has been trapped due to the currents of the North
Pacific Gyre. The problems posed by the Great Pacific
Garbage Patch are numerous, but, more often than not,
they remain unknown to the general population. To further explain, it is important to clarify what exactly the
Great Pacific Garbage Patch is, and how it has come to be
of floating plastic to cover roughly the size of Texas.”2
The Garbage Patch, located in the central North Pacific
Ocean, was revealed to have enormous amounts of plastic debris floating near the surface. The majority of the
plastic found in the Garbage Patch is very small, typically being no larger than 5 mm in length.
The Great Pacific Garbage Patch is located in an
area where environmental and man-made factors have
caused it to become the world’s largest landfill. The currents of the North Pacific Gyre create a vortex, leading
to a convergence zone where nearly all matter caught
in the currents becomes trapped. According to the Na-
Stephen Jenkins studies Global Environmental Change and Sustainability at Johns Hopkins University.
23
JOHNS HOPKINS
tional Oceanic and Atmospheric Administration, “80% of
oceanic pollution originates from land. This is where
humans come into play.”3 Improper waste disposal and
negligence regarding the manufacturing of plastics are
both significant contributors to oceanic debris. The natural currents of the Pacific Ocean in combination with
societal factors have created the Great Pacific Garbage
Patch.
Previously, it was thought that plastics only broke
down at very high temperatures over a long period of
time. Contrary to this belief, in 2009 Japanese researchers found that “[plastic] degraded at temperatures of 86
degrees Fahrenheit”, and “breaks down…within a year of
the trash hitting the water.”4 This creates problems for
many reasons. The degradation of plastics is thought to
release many potentially toxic chemicals into the ocean,
them. These animals depend on the nutrition that the
ocean provides and oftentimes cannot distinguish between plastic and food. About “44 percent of all seabirds
eat plastic, sometimes with fatal effects. In total, an estimated 267 marine species are affected by plastic.”8 When
large amounts of plastics are found within animals, the
animals are not only being deprived of nutrients, but
also faced with health problems such as digestive tract
issues. According to the United Nations Environment
Program, it is estimated that “1 million seabirds and
100,000 marine mammals and turtles die per year due to
the ingestion of plastic.”9 These statistics help reveal the
damage that plastic does to marine life.
The issue of cleaning up the Great Pacific Garbage
Patch has troubled scientists since its discovery. Fortunately, many non-profit organizations with the goal of
The Great Pacific Garbage Patch is located in an area where
environmental and man-made factors have caused it to
become the world’s largest landfill.
including bisphenol A. The release of BPA into the water is a danger to marine life and to humans as well.
Research, titled the Lang Study, collected between the
years 2003-2006 indicated that “exposure to BPA raises
the chance of coronary heart disease in adults.”5 A similar study to replicate the results of the Lang study provided almost identical data; “adults who [had] the highest
concentration of BPA within their urine had a 33% higher chance of suffering from coronary heart disease.”6
Other research has also been conducted on the potential dangers of BPA. A 2008 study that was published in
the Proceedings of the National Academy of Sciences
concluded that “BPA acts as an inhibitor of spinal synapse formation in the hippocampus and the prefrontal
cortex.”7 Previous research had been done on this issue using mice, but the 2008 study used adult African
Green Monkeys to show the probable harm that BPA
could cause within humans. The researchers exposed
the monkeys to 50 μg/kg of BPA per day. This number
was selected because it falls within the daily safe limit
as suggested by the EPA. Even at this recommended safe
amount of exposure, research seems to indicate that it
could have a harmful effect on primates. Although the
exact effects are not completely understood, “alterations
in patterns of synaptogenesis appear to play critical
roles in neurologic disorders, including mental retardation and developmental disabilities, Alzheimer’s disease,
schizophrenia, and mood disorders.”7
There lies another, more evident problem with the
Great Pacific Garbage Patch. Birds of many species and
other marine animals feed on whatever is available to
24
confronting this problem are becoming increasingly
prominent in the world of environmental sustainability. One of these organizations is the Environmental
Cleanup Coalition. Founded in 2008, this organization
has brought together partners that promote the continuing health of our oceans. Project Kaisei is one such
non-profit organization that is focused on increasing
awareness of the scale of marine debris, its impact on
our environment, and the solutions for both prevention and clean-up.10 The SCRIPPS Institute based out of
the University of California San Diego is another organization with goals similar to Project Kaisei. Working
together, the two groups funded the SEAPLEX voyage.
The goal of SEAPLEX is to survey the distribution of
1 million seabirds
and 100,000 marine
mammals and turtles
die per year due to the
ingestion of plastic.
plastic in the area that the Pacific Garbage Patch comprises and discover the impact of plastic debris on local
fauna. SEAPLEX was completed in August 2009 and saw
the two organizations travel a distance of 1,700 miles
into the Pacific Ocean from their starting point of San
Diego. During this time “small plastic debris was found
in 130 out of 132 surface sample nets that were used for
regular analysis over the course of the expedition.”11
This joint effort is the world’s largest attempt to collect
crucial data on the Pacific Garbage Patch. All of their
information has been passed on to the NOAA which is
looking into the potential effects and harm that the plastic causes.
Similarly, the Abundant Seas Foundation researches potential cleaning
methods using environmental engineering. Partnering with the ECC, the
Abundant Seas Foundation has done
work on the Pod Project, an effort to
launch the Pelagic Pod into polluted
waters. The Pods used in the project
are made of recycled plastic with a design similar to an ocean buoy. They are
powered by solar panels that are outfitted on the exterior of the pod, while
the inside draws plastic particles into
the chamber and a proprietary mesh
that entangles the particles for permanent removal. The design allows for
small materials to be filtered through,
while larger organisms, such as fish,
are safe from being trapped. “Water is
directed downward into the Pod’s internal chamber. Inside the Pod, a density
separation process and a plastic micro-fiber scrubber
will remove the plastic particles from the seawater.”12
In addition to filtering microplastics, the pods help restore the marine ecosystem by acting as an anchor point
for biomass. Fertilization of the water will be achieved
by two methods: first, by releasing iron into the water
from its scrap metal ballast, and second by releasing nutrient rich biscuits that are made from sterilized and
compressed bio-solid derivatives from terrestrial wastewater treatment systems. Although still in the prototype
phase, it is likely that these pods will be able to collect
JOHNS HOPKINS
microplastic debris without disturbing the natural environment. Mass production of this tool will become essential as the biggest obstacle to cleanup efforts in the
past has always been the potential damage to the natural
ecosystem inhabiting the same area. Research and development is still in the infancy stage, there is hope for the
future as more data becomes available.
It is commonly accepted that the Great Pacific Garbage Patch poses a problem to the environment, but the
exact nature and enormity of the issue is difficult to ascertain. As a result, the Garbage Patch remains largely
mysterious to researchers today. Due to the relatively
small number of studies that have been conducted on
the subject, it is difficult to determine long-term effects,
as well as potential methods of cleanup. Luckily, the issue is gaining widespread notoriety and there are now
many organizations that are looking to combat the problems that the Garbage Patch poses.
references
1. Browne M., Crump P., Niven S., Teuten E., Tonkin A., Galloway T., et. al. Accumulation of Microplastic on Shorelines Woldwide: Sources and Sinks. ACS Publications
[Internet]. 2011 [cited 2011 December 6]; [approx. 1 p.]. Available from: http://pubs.
acs.org/doi/abs/10.1021/es201811s?prevSearch=%255BContrib%253A%2Bmark%2Bbrowne%255D&searchHistoryKey=
2. Greenpeace International (NL). The trash vortex [Internet]. Amsterdam (NL): Greenpeace International; [cited 2011 December 8]. Available from: http://www.greenpeace.
org/international/en/campaigns/oceans/pollution/trash-vortex/
3. National Oceanic and Atmospheric Administration (US). Most Ocean Pollution Begins
on Land [Internet]. Silver Spring (MD): U S Department of Commerce; 2011[updated
2011 Nov 17; cited 2011 December 5]. Available from: http://oceanservice.noaa.gov/
facts/pollution.html
4. Barry C. National Geograpic Society (US). Plastic Breaks Down in Ocean, After All
– and Fast [Internet]. Washington (DC): National Geographic Society; 2009 August
20 [cited 2011 December 6]. Available from: http://news.nationalgeographic.com/
news/2009/08/090820-plastic-decomposes-oceans-seas.html
5. Lang I. , PhD; Galloway T., PhD; Scarlett A., PhD; Henley W., PhD; Depledge M., PhD,
DSc; Wallace R., MD; et. al. Association of Urinary Bisphenol A Concentration With
Medical Disorders and Laboratory Abnormalities in Adults. JAMA [Internet]. 2008
[cited 2011 December 8];300(11):1303-1310. Available from: http://jama.ama-assn.org/
content/300/11/1303.full
6. Melzer D., Rice N., Lewis C., Henley W., Galloway T. Association of Urinary
Bisphenol A Concentration with Heart Disease: Evidence from NHANES 2003/06.
PLoS ONE [Internet]. 2010 January [cited 2011 December 8];5(1):1-9. Available
from: http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0008673&representation=PDF
7. Leranth C., Hajszan T., Szigeti-Buck K., Bober J., MacLusky N. Bisphenol A prevents
the synaptogenic response to estradiol in hippocampus and prefrontal cortex of
ovariectomized nonhuman primates. PNAS [Internet]. 2008 Sep [cited 2011 December
10];105(37) [approx 4 p.]. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/
PMC2544599/?tool=pmcentrez#__sec6
8. Greenpeace International (NL). Plastic Debris in the World’s Oceans [Internet]
Amsterdam (NL): Greenpeace International; [cited 2011 December 7]. Available from:
http://www.greenpeace.org/austria/Global/austria/dokumente/Studien/meere_Plastic_Debris_Study_2006.pdf
9. Gjerde K., Ecosystems and Biodiversity in Deep Waters and High Seas. UNEP [Internet]. 2006 [cited 2011 December 8]; 178: 54. Available from: http://www.unep.org/pdf/
EcosystemBiodiversity_DeepWaters_20060616.pdf
10. Project Kaisei (US). Kaisei History [Internet] San Francisco (CA): Project Kaisei; [cited
2011 December 9]. Available from: http://www.projectkaisei.org/kaisei_history.aspx
11. Scripps Institution of Oceanography (US). SEAPLEX [Internet] San Diego (CA):
Scripps Institution of Oceanography; 2009 [cited 2011 December 9]. Available from:
http://sio.ucsd.edu/Expeditions/Seaplex/Science/
12. Abundant Seas Foundation (US). Pod Project [Internet] Gig Harbor (WA): Abundant
Seas Foundation; 2009 [cited 2011 December 9]. Available from: http://abundantseas.
org/pod_project
13. http://nerdswithoutborders.net/index.php?title=File:Hawaii_turtle_2.JPG
25
REPRODUCED FROM [7]
CORNELL
The New “Black Gold”:
Biochar
Jennifer Sun
as battles over greenhouse gas emissions, renewable energy technologies, climate change, land degradation, and a host of other environmental issues continue,
researchers and policy makers have begun to look towards more aggressive approaches for developing sustainable practices. In recent years, one new technology
has emerged as a promising method of not only sequestering carbon, but also simultaneously improving agricultural soil fertility and producing energy. Biochar, or
a charcoal formed during the slow burning of woody
biomass, has been used for hundreds and thousands of
years in nutrient-poor soils in the Amazon Basin and
more recently in Japan as a fertilizer in nutrient-poor
soils in these regions.5 Within in the past few years,
however, biochar has risen to international attention as
a potential carbon-capture and soil amendment technology that can be used on both local and industrial scales.
Biochar, or “black carbon,” is a concentrated carbon
product derived from the slow pyrolysis of biomass.
This process of biochar production builds upon the concept of burning biomass instead of fossil fuels for energy, which reduces carbon emissions by recycling carbon
between recently grown biomass and fuel combustion,
rather than releasing carbon from a long-term carbon
pool. Instead of combusting biomass to produce heat,
however, in pyrolysis woody biomass is burned at low
temperatures with little or no oxygen. This process produces bio-oils and drives off gases such as carbon monoxide and hydrogen, which can be captured and either
burned to produce heat or further processed to produce
other forms of energy.5 What is left behind is biochar,
or a charcoal in which carbon has been concentrated
to twice its original levels.1,3 This concentrated carbon
product can either be burned to produce more electricity, or added to agricultural fields as a soil addition.
26
Jennifer Sun studies the Science of Natural and Environmental
Systems, with a concentration in Environmental Biology, at Cornell
University.
It is through this use as an agricultural amendment
that biochar truly distinguishes itself from other carbon-capture technologies.5 While the gas products
of pyrolysis can still be captured to offset the energy
needed to produce the biochar, the remaining carbon in
the char will be sequestered underground. Furthermore,
biochar application dramatically reduces methane and
nitrous oxide emissions from microorganisms in soil,
both of which are even more potent greenhouse gases
than carbon dioxide.4 As a result, biochar can be classified as a net carbon-negative process under the Kyoto
Protocal standards.4 As an organic product, biochar also
helps improve soil quality and fertility, improving agricultural production and helping to restore degraded
soils for agricultural use.1 For example, biochar helps
retain water and associated nutrients in soil, while reducing soil erosion and general soil degradation. This
not only increases crop yields, but also reduces the
need for additional chemical fertilizers, which not only
reduces energy and production costs, but also reduces nutrient leaching and associated water pollution that
can cause algal blooms and fish kills.1,6 By maintaining
soil quality and fertility over a longer period of time,
biochar will help agricultural areas support growth for
longer, slowing the process of deforestation for agricultural expansion in many developing nations.1
Because biochar is an organic product, it is acknowledged that it will eventually decompose and release carbon back into the atmosphere. Once buried in soil, however, biochar is estimated to remain stable for hundreds,
or potentially thousands, of years.2,3 On the timescale
of carbon-capture and storage, this is considered to be
a long-term sequestration technology: in comparison,
other carbon storage methods such as afforestation or
no-tillage agriculture have storage capacities only on
the order of a few years to decades.1 As a result, this net
carbon-negative product has generated considerable interest as a potential carbon-offset technology, which can
help generate revenue through the carbon trade market
to help maintain the cost of biochar production.
At least 150 current biochar projects have been
identified in 43 countries
As with any energy—or emissions—reduction technology, the level of success and economic viability of
biochar depends on a variety of factors, including the
availability of cheap feedstocks and a market for the bioenergy and carbon credits produced by biochar production.1, 4 Dr. Johannes Lehmann, Chairman of the International Biochar Initiative Board and Associate Professor
in the Department of Crop and Soil Sciences at Cornell,
estimates that the use of forest residues, crop residues,
or fast-growing vegetation grown on currently idle cropland in the US to produce biochar could sequester 10%
of current US carbon emissions.1 However, though the
development large-scale production of biochar may still
encounter some economic barriers, one great benefit
of biochar over other technologies is that the pyrolysis
process is already well developed, having been used previously for energy production. The process is also very
flexible and can utilize a wide variety of biomass feedstocks, including agricultural and forestry wastes, urban
wastes, and crop residues in addition to purposefully
grown biomass such as corn stover and miscanthus, a
species of perennial grass. As a result, small-scale production of biochar is ideal for use in developing countries, particularly in the tropics where nutrient content
in soils is relatively low.1,6 Recently, Cornell University
and the International Biochar Initiative have been working with the World Bank to identify potential new target
regions that may be able to benefit from biochar application. So far at least 150 current biochar projects have
been identified in 43 countries, including Chile, Uganda,
Kenya, Sri Lanka, and many others.6
Though the concept of biochar has been known for
a few decades, biochar has only recently been seriously
recognized as a potential carbon-capture technology in
the past 5 or 6 years.5 Since then, a number of energy
bills that have been introduced to the Senate have included provisions for the funding of biochar research
and its inclusion as an approved carbon-offset technol-
CORNELL
ogy, including the Water Efficiency via Carbon Harvesting and Restoration (WECHAR) Act of 2009, which was
specifically aimed at funding biochar research and projects.6 Industrial-scale biochar production has also begun
to grow rapidly, with new plants being produced in Brazil, Japan, and China within the past couple of years.5
Finding the resources, political support and funding
to develop biochar production and sequestration still
present a major challenge towards developing biochar
to its full potential. Proponents of the technology do not
attempt to claim that it will be the panacea for our climate change challenges, but at least in the near-term it is
likely to play an increasingly important role in providing a variety of benefits—energy production, improved
soil quality and carbon capture—in localized regions
worldwide. Indeed, the lack of need for new technology
or synthetic chemicals, the ability to utilize a variety of
biomass feedstocks, and the myriad of ecological and
economic benefits offered in addition to carbon capture make biochar a particularly attractive technology.
Though ultimately carbon sequestration may only be
moderate-term solution, improved soil fertility can be
relied upon. Whether for short- or long-term environmental benefits, biochar as a multi-use technology will
likely play a role in combating greenhouse gas emissions
and soil degradation in both developed and developing
nations in coming years.
REPRODUCED FROM [8]
references
1. Lehmann J. A handful of carbon. Nature. 2007; 447: 143-144
2. Ammontte J, Lehmann J., and Joseph S. Terrestrial Carbon Sequestration with Biochar: A Preliminary Assessment of its Global Potential. American Geophiysical
Union. 2007. Abstract.
3. Gaunt JL, Lehmann J. Energy Balance and Emissions Associated with Biochar
Sequestration and Pyrolysis Bioenergy Production. Environ. Sci. Technol. 2008,
42 (11): 4152-4158.
4. Gaskin JW, Steiner C, Harris K, Das KC, Bibens B. Effect of Low-Temperature
Pyrolysis Conditions of Biochar for Agricultural Use.
5. Lehmann, J. Personal communication. 21 Oct 2011.
6. International Biochar Initiative [Internet]. [cited 21 Oct 2011]. Available from:
http://www.biochar-international.org/
7. http://commons.wikimedia.org/wiki/File:Charcoal2.jpg
8. http://spin-project.eu/img/12043_Ecoera_biochar_ladybug.JPG
27
CORNELL
Reading Reinvented:
How Computers and the Internet are
Influencing our Society
Latha Panchap
in the mind of the average computer user, the
internet has the answers to almost all of life’s questions.
Between the search engines and the millions of constantly updated webpages, the internet gives users the
ability to know everything that has happened, is happening, and might happen, all at their fingertips. This is the
internet’s greatest gift: unlimited information. However,
recent discoveries about the internet’s effect on Americans’ reading skills show that such technology may have
significant repercussions on society and today’s youth.
A 2010 study from the Pew Research Center shows
that Americans spend an average of 60 hours a month
on the Internet. American internet users spend 42% of
this time viewing internet content, such as blogs and articles.1 The growing concern among parents and teachers, however, is that this time spent surfing Fanfiction.
net or Tumblr could be used to do something more intellectually stimulating.2 A study released in 2004 by the
National Endowment of the Arts (NEA) indicates that
the decrease in the number of novels read by teenagers
may be a crucial reason for the drop in standardized
28
Latha Panchap is studying Biological Engineering and Business at
Cornell University.
reading test scores.3 Chairman of the NEA, Dan Gioia,
believes that the Internet and its many distractions may
be one of the main sources of this decline, signified by
his statement “[The benefits of newer electronic media]
provide no measurable substitute for the intellectual
and personal development initiated and sustained by
frequent reading.”2
Gioia’s claim brings up an interesting point: What
exactly is the difference between reading in print and
reading online? In their book The Myth of the Paperless Office, cognitive psychologist Dr. Abigail Sellen and
researcher Richard Harper come to the conclusion that
navigating a webpage requires more brain power than
turning the pages of a novel. Furthermore, the light-producing screens of computers force our eyes to constantly focus and refocus.4 This difficulty alone causes users
to read 25% slower on screen than on paper.5 In addition,
the many distractions of the internet cause readers to
lose ‘flow’, a term used by psychology professor Dr. Mihaly Csikszentmihalyi to describe “a deep but effortless
involvement that removes from awareness the worries
and frustrations of everyday life.” Paper novel enthusiasts can identify with this familiar feeling: becoming immersed in a novel and losing all sense of time. This state
of full absorption in reading is difficult to achieve with
a computer. Instant messages, emails, music, and pop-up
ads distract us and cause frequent breaks in our ‘flow’.4
Attention blindness is a crucial part of achieving
‘flow’. Cognitively, this can be explained through the actions of neurons. Neurons fire off in pathways to complete certain actions, such as reading. As these pathways
are repeated more often, the neurons link together, and
the actions are performed more efficiently. Eventually,
these actions become automatic reflexes that pass undetected under our radar of attention. This is known
as attention blindness. Reading is an automatic reflex,
meaning that our neurons are already wired together
in efficient pathways to do this task. Because of this, we
are subject to attention blindness while reading. Profes-
sor Cathy Davidson feels that people pay attention to
actions, responses, and ideas for which their neurons
have not formed pathways. Therefore, when pop-ups or
instant messages appear on the screen, we automatically pay more attention to these distractions than to the
text.6
The internet’s negative effects go much deeper than
distracting and taxing the user. In his article “Is Google
Making Us Stupid?” Nicholas Carr voices the worry that
Instant messages,
emails, music, and popup ads distract us and
cause frequent breaks in
our ‘flow’
many readers now have— that the internet is influencing the way we process information. According to Carr,
we no longer possess the focus and thought to deeply understand what we are reading, only the ability to
skim and superficially grasp the meaning of the text.7
Dr. Jakob Nielsen, who holds a degree in human-computer interactions, claims that humans’ method of reading
has actually changed— our new reading pattern consists of web searches and scanning, paying attention to
CORNELL
small paragraphs, bolded words, headings, and lists.8 His
eyetracking study, which observed the eye movements
of 232 users, showed that people scan websites using a
rough F-pattern, reading the first two paragraphs and
then scanning the left side of the page.9 Nielson’s conclusion is that computer users have become ‘information foragers’. Like jungle animals scavenging for food,
we’ve learned to scan websites for information, find
what we need, and move on to the next website.10 Search
engines like Google and Bing have encouraged this process by organizing pertinent webpages into one list and
giving snippets of text to summarize the contents of
each site. Google’s desire to create “the perfect search
engine” consequently takes all the work out of actively
searching for information and discourages people from
exhausting a single source before finding another.7
Proponents of this internet revolution argue that the
benefits of the internet far outweigh the aforementioned
repercussions. Experts in early childhood development
claim that the interactive interface of the internet promotes the development of literacy and problem-solving
skills, as well as the ability to synthesize information
from multiple sources.11 Educators supporting the use
of the web as a reading medium believe that it can also
provide many different perspectives and a wider, more
comprehensive view of a subject. Computer-based reading’s strong influence on American children caused literacy experts to advocate the addition of a computer
component to the Nation’s Report Card, an annual study
29
CORNELL
conducted to measure the proficiency of the nation’s
youth in a variety of subject areas.2
Mr. Jonathan Senchyne, a doctoral candidate in English at Cornell University, believes that the ability to
instantly share and edit information is another huge advantage of internet reading (J. Senchyne, personal communication, October 27, 2011). The invention of blogs
and other types of self-publish sites has granted everyone the ability to express their opinion to the world at
large. Wikis, for example, have become a popular way
for people to share the information that they have and
learn from what others have posted. Although this content may not always come from a reliable source, studies show that the collaboration of many individuals on
one subject’s Wiki page can lead to very accurate content. Wikipedia, for example, was found to have an error
rate close to that of Encyclopedia Britannica, a highly-regarded scholarly encyclopedia. However, Wikipedia
differs from Encyclopedia Britannica in that if found,
these errors can be fixed immediately by anybody with
internet access.12 Senchyne believes that this type of instant sharing and editing has allowed computer users,
especially students and younger children, to become
“social readers” who now read the article, then discuss
it in forums with one another.
Access to unlimited information and multiple perspectives makes the internet an invaluable source for
young Americans in the process of developing synthesis and problem-solving skills. However, the internet’s
many distractions and its complicated interface can
cause us to lose focus on what we are reading. Over the
years, our brains have learned to overcome these challenges by skimming articles for answers instead of gaining a deep understanding of the text. As the influence of
the internet continues to grow, the differences between
reading paper text and reading online will become more
pronounced, as will the effects of web-based reading on
the way we read, write, think, and communicate. During
this revolution, we must stay aware of these differences
and either learn to adapt our daily lives to this new system of thinking or find a way to control the degree to
which the internet influences our daily lives.
references
1. Smith C. Internet Usage Statistics: How We Spend Our Time Online (INFOGRAPHIC). Huffington Post [Internet]. [homepage on the Internet]. 2010 Jun 22 [cited 2011
Oct 3]; Tech: [about 2 screens]. Available from: http://http://www.huffingtonpost.
com/2010/06/22/internet-usage-statistics_n_620946.html
2. Rich M. The Future of Reading - Literacy Debate - Online, R U Really Reading?. The
New York Times [Internet]. 2008 Jul 27 [cited 2011 Oct 07]; Arts [about 10 screens].
Available from: http://www.nytimes.com/2008/07/27/books/27reading.html?pagewanted=all
3. Rich M. Study Links Drop in Test Scores to a Decline in Time Spent Reading. The
New York Times [Internet]. 2007 Nov 19 [cited 2011 Oct 02]; Arts [about 3 screens].
Available from: http://www.nytimes.com/2007/11/19/arts/19nea.html?adxnnl=1&ref=books&adxnnlx=1326294343-Nkr+Fh/sP757DBsEwL2+sQ
4. Powers W. Hamlet’s Blackberry: Why Paper is Eternal. Joan Shorenstein Center on
the Press, Politics and Public Policy Discussion Paper Series. Cambridge: Harvard
College; 2007. p. 1-74.
5. Nielsen J. Useit.com: Jakob Nielsen’s Website. [homepage on the Internet]. 1997 [cited
2011 Sep 30]. Why Users Scan Instead of Read; [2 screens] Available from: http://
www.useit.com/alertbox/whyscanning.html
6. Davidson C. Now You See It: How the Brain Science of Attention Will Transform the
Way We Live, Work, and Learn. New York: Viking; 2011.
7. Carr N. Is Google Making Us Stupid?. The Atlantic [Internet]. 2008 [cited 2011 Oct
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02]; Magazine: [about 8 screens]. Available from: http://www.theatlantic.com/magazine/archive/2008/07/is-google-making-us-stupid/6868/
2011 Sep 30]. How Users Read on the Web; [3 screens] Available from: http://www.
useit.com/alertbox/9710a.html
2011 Sep 30]. F-Shaped Pattern For Reading Web Content; [3 screens] Available from:
http://www.useit.com/alertbox/reading_pattern.html
2011 Sep 30]. Information Foraging: Why Google Makes People Leave Your Site Faster; [4 screens] Available from: http://www.useit.com/alertbox/20030630.html
11. Johnson G. Internet Use and Cognitive Development: a Theoretical Framework.
E-Learning Digital Media. 2006 [cited 2011 Oct 25] 3(4): [8 pages]. Available
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13. http://commons.wikimedia.org/wiki/File:Great_Books.jpg
ACKNOWLEDGEMENTS
The Triple Helix Cambridge would like to thank the following colleges and groups for their generous continued support.
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and Caius
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The Department of History and Philosophy of Science
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The Cambridge Philosophical Society
Christ’s
Newnham
St. John’s
Magdalene
cambridge philosophical society – lent 2015
Lighting the Future: Next generation
LED lighting to save energy and
improve our health
Monday, 9 February
6 p.m. – 7 p.m.
Professor Sir Colin Humphreys
CBE FREng FRS, Department of Materials Science
www.cambridgephilosophicalsociety.org
[email protected]
01223 334743
a v hill lecture
Science and the quiet art revisited
Between rock and a hard place:
soil, the ambiguous material
Monday, 23 February
6 p.m. – 7 p.m.
Monday, 9 March
6 p.m. – 7 p.m.
Professor Sir David Weatherall
Professor Malcolm Bolton
Institute of Molecular Medicine, University of Oxford
All events are in the Bristol-Myers Squibb Lecture Theatre, Department of Chemistry.
Lectures are open to all who are interested.
If you are interested in supporting The Triple
Helix’s mission financially or otherwise, please
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© 2015 The Triple Helix, Inc.
All rights reserved.
FREng, Department of Engineering
The Triple Helix Cambridge is an independent chapter of The
Triple Helix, Inc., an educational 501(c)3 non-profit corporation. The Science in Society Review is published once per term
by the Triple Helix Cambridge and is available free of charge.
Its sponsors, advisors, and the University of Cambridge are not
responsible for its contents. The views expressed in this journal
are solely those of the respective authors.
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