9.1
A Brief History and Overview
9.2
The Bio-Sciences Report (c. 2180)
9.3
The Bio-Weapons Report (c. 2185)
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Entry 9.1
A Brief History
and Overview
 The
DNA Reflex (originally termed: "Invasive DNA Assimilation and Modification
Reflexive Behavior") was a notion presented by the Weyland-Yutani
Biological-Sciences Division in 2180 as a means to explain the Alien's
ability to acquire gross anatomical traits from a host through modifications
of that host's DNA. This theory - even in light of the events of Fiorina
161 - was initially regarded by the scientific communities, as "ridiculous"
and "idealistic" due to the fact that it relied heavily on
theoretical genetics. It did, however catch the attention of Colonel
Jason C. Abbot, the head of Weyaland-Yutani's Biological-Weapons Division
at that time. Despite the public's rejection of the theory, Colonel
Abbot pressed several teams of Bio-Weapon engineers to begin further
study into the plausibility and possibility of Internecivus Raptus
employing what had unofficially become known as the DNA Reflex. Given
a three-year timetable Abbot's teams worked under tight security to
continue what the Bio-Sciences Division had started. As research continued
it became increasingly apparent that what the Bio-Sciences Division
had tapped into was not only plausible and possible, but the implications
of the Alien's adaptation were both far reaching and terrifying.
In 2183 a Classified
Report entitled "The DNA Reflex" was issued - it outlined
the three year research of Abbot's teams. Little is known of what happened
to the report following its release, but it is known that Colonel Abbot
met with Brigadier General James L. Carson, Brigadier General Shelly
P. Abraham, and Major General Wendy A. Martinez 24 hours following its
release. 48 hours after this meeting a second Clean-Up and Examination
crew was dispatched to Fiorina 161, and a Survey team was assembled
and sent to LV-426 - both teams consisted of several exobiologists,
archeologists, geneticists (specializing in pathogens), and a compliment
of USCA Corp. of Engineers.
In 2185 the newly
promoted Brigadier General Abbot released an updated form of "The
DNA Reflex" to The Bio-Sciences Division with one additional copy
going to the head of Weyalnd-Yutani's Special Projects Division - Rachel
Cross. Unaware of the previous report, it was believed by the scientific
community that this was the first release of this material - it was
hailed as a triumph in further understanding I. raptus, and quickly
became the excepted theory. We know now that what General Abbot released
was a modified version of the original report form 2183. Material deemed
"Sensitive" as well as additional findings from Fiorina 161
and LV-426 were not included, or only mildly incorporated so as to keep
the reports up-to-date. It is believed that the complete version of
"The DNA Reflex" from 2185, was deemed "Classified"
by General Abbot, and subsequently withheld from the public. As a credit
to Abbot's teams and the follow-up missions to Fiorina 161 and LV-426
it is further believed that it was Abbot's classified documentation
that spurred Dr. Wren's research nearly 200 years later.
Over the following
years, as Dr. Wren studied the recovered samples of blood and tissue
from Fiorina 161, what was found was that the Alien embryo is not only
a member of the deadly symbiosis with its host, but the host's genetic
coding undergoes a process such that it is almost completely re-written.
It is still not fully understood how such a drastic change can occur
within an extremely short span of time (presumed to be 4 to 6 hours).
It is also still not clear what percentage of the Alien's genetic code
is infused into the host's. It has been presumed that Dr. Wren was aware
of this, to some degree, and had documentation to accompany his findings
- however, these records were either lost in the Auriga's destruction,
or are classified by the United Systems Military. What was available
of Dr. Wren's work showed that the genetic modifications not only force
the host organism to create the Alien embryo much in the way it would
a cancer, but enhance aspects such as the host's immune system.
In the medical
records obtained from Fiorina 161 following Lieutenant Ripley's arrival:
Lieutenant Ripley had been diagnosed with Post Traumatic Hibernation
Disorder - a short-term illness caused by a sudden and improper awakening
from hyper-sleep. The symptoms range from coma to disorientation accompanied
by headaches, soar throat, cough, and/or nausea and vomiting - depending
on the severity of the case. The symptoms of this disorder can last
anywhere from 3 to 10 days - again, depending on the severity of the
case. Lieutenant Ripley was diagnosed with slight disorientation, soar
throat, cough, nausea, and minor headaches. She was also diagnosed with
minor abrasions and lacerations, and the subcutaneous rupture of blood
vessels throughout the cornea of the left eye. Within a matter of 8
hours all recorded symptoms - with the exception of a few lacerations
- had completely healed. However, since there was even less understanding
of the Alien and its capabilities at that time the healing of Lieutenant
Ripley's wounds and symptoms was not associated with the presence of
an I. raptus embryo.
The following entries
include material from the report issued by Weyland-Yutani Bio-Sciences
Division in 2180, as well as the public report released by Abbot's teams
in 2185. Both are represented to better display the differences in approach
between the two divisions, and how we achieved the theories we now have
and use.
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Entry 9.2
The Bio-Sciences
Report (c. 2180) The
incorporation of theoretical genetics was only part of what kept the
Bio-Sciences Division's approach from being accepted. The other part
was that their approach looked to the Alien embryo as being an extension,
or continuation of the host body - much in the way any internal organ
or body part is. This stemmed from a view that the first stage of I. raptus (the Facehugger) was treating the host organism as an in vitro
womb, as opposed to a host. This is rather ironic considering the fact
that they compared the incorporation of I. raptus DNA to being like
a virus.
Excerpt from "Invasive
DNA Assimilation and Modification Reflexive Behavior," Submitted
by Weyland-Yutani Biological Sciences Division, 18.12.2180:
 "The
process by which [Internecivus Raptus] is able to successfully
alter its host's DNA so as to create a more suitable host environment
(and presumably to create an offspring that is better suited to
adapt and prey upon a specific organism and its environment) is
still under a certain degree of speculation. The lack of data received
from Fiorina 161 and LV-426 has made the process of determining
how the altering of a host's genetic code is done a difficult task.
It is proposed that the process is done in a manner analogous to
a virus.
In this process
it is believed that I. raptus genetic material "invades"
a host's DNA, which alters gene expression and activation. As this
process occurs new genes are created, forcing the cells to function
and exist in a manner that is more suitable to the development of
an I. raptus embryo. It is also proposed that as this forced change
occurs new proteins and amino acids are produced - creating a host
environment that is drastically different than the original (even
if only on the cellular/sub-cellular level).
The means by
which I. raptus is able to invade a host's DNA is not fully known,
but it is proposed that this is done via the introduction and utilization
of a DNA polymerase-like enzyme. In its common state a DNA polymerase
is an enzyme that catalyzes the replication and repair of existing
DNA in an organism by using a single stranded DNA as a template.
The simple act of introducing such an enzyme into a host organism
would not result in the eventual restructuring of the DNA in a manner
that would enable an I. raptus embryo to survive and develop. Nor
would it cause the modifications to a host organism's DNA resulting
in the anatomical abilities/modifications that were recorded in
the Fiorina 161 medical reports of Lieutenant Ripley following her
recovery. For such a DNA polymerase to create the type of genetic
restructuring that is apparent in the initial stages of the I. raptus
life cycle the enzyme would need to contain both Alien and host
coding - in order for this to happen some kind of genetic splicing
would need to take place. Commonly, for DNA recombination to occur
a minimum of 2 enzymes are required: a Restriction Enzyme, which
is responsible for cutting the DNA at specific nucleotide sequences,
and a DNA Ligase for "stitching" the newly inserted DNA
material into the original host material. Of course, in order for
this to work the inserted genetic material needs to be compatible
and compliment the existing DNA - if it's not then serious restructuring
of the host and foreign DNA needs to occur. It's thought that the
Alien's efficiency in existence may be traceable all the way down
to its genetic base. By this it's believed that even with the creature's
complex physiology it may employ a relatively simple yet efficient
genetic structure. One that is highly adaptable/modifiable to the
point of being almost a generic genetic template that can accept
nearly any DNA chain that it is presented with.
The DNA polymerase-like
enzyme that I. raptus would introduce into a host system has been
referred to as a "Hyper-Aggressive Enzyme." The working
model for this enzyme revolves around the notion that it's an incomplete
structure that not only replicates DNA strands upon contact, but
also splices and restructures as well. The idea is based on the
thought that the process a DNA polymerase undergoes to replicate
existing DNA is only a step away from DNA Recombination under the
correct circumstances: i.e. the process of DNA replication is basically
a form of DNA splicing and combination - in and of itself - among
existing genetic elements. The incorporation of an outside genetic
element is theoretically only another step away. If I. raptus is
able to employ such a genetic feat this would mean that is has mastered
something that current human science has yet to control. For nearly
200 years geneticists have struggled with the possibility of creating
such an enzyme in a controlled laboratory so as to aid in new directions
of DNA recombination for medicinal purposes.
 The
incomplete aspect of the enzyme is what would make it aggressive:
It has been speculated that one of the means by which the Alien
is able to incorporate its own DNA into a host system is through
requiring specific proteins. Enzymes are, by nature, an arrangement
of complex proteins. The Hyper-Aggressive Enzyme may actively seek
out various proteins from a host system in order to initiate DNA
restructuring, and its own completion. It is believed that this
enzyme is inert and otherwise inactive in its "natural"
state, but once introduced into an environment that contains various
proteins it moves from an inert state to an active state. To say
that it actively seeks out these proteins may not be an accurate
description: It may be attracted to such proteins and otherwise
aggressively incorporate them into its own structure. This pattern
would follow that of various viruses once they are introduced to
a host system. Once the hyper-aggressive enzyme has acquired the
necessary proteins from the host the catalyst can begin, and the
enzyme is able to begin DNA restructuring and replication - all
the while incorporating Alien and host proteins. To aid in a successful
fusing of genetic material. As new DNA is modified, and effectively
re-written, the expression of new proteins occurs, along with the
creation of additional Hyper-Aggressive Enzymes. Given the speed
at which I. raptus is able to develop it is believed that the spread
of this enzyme through a host system is extremely pervasive.
Of course,
this is strictly theoretical, and the mere acquisition of host proteins
would not be enough to initiate, or facilitate the type of genetic
restructuring that apparently goes on within a host system so as
to create an I. raptus embryo. The means by which a conceivably
incompatible genetic structure could be grafted, or spliced into
a host system is not fully understood. There still remains the issue
that in order for recombinant DNA to function properly the combined
pieces must have complimentary ends and elements that readily combine
with each other. Given the physiology of the Alien it does not seem
likely that it's DNA would compliment a wide array of hosts. Thus,
it is proposed that the Alien incorporates a simple - or generic
- genetic structure that is easily compatible, or modifiable, with
varying host organisms."
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Entry 9.3
The Bio-Weapons
Report (c. 2185)  Colonel
Abbot immediately saw a potential in the above material. Understanding
why it was being summarily dismissed by the scientific community he
decided to follow through with what the Bio-Sciences Division had not
done in their haste to release their reports to the public: explore
other known means of genetic modification to find a link as to how I. raptus is able to achieve the DNA Reflex. Of course some aspects of
theory had to be employed, but his teams focused on processes that were
known to exist.
Towards the end
of the tree years that Abbot's teams strove to find a viable answer
to DNA modification a different approach was employed. As opposed to
viewing the Alien embryo as an extension of the host organism it was
seen as a mutation - a malignant growth as a direct result of a terminal
illness brought on by genetic modification. Once this view was considered
theories began to arise that would not only become an excepted belief,
but presumably catch the attention of the Dr. Wren.
Excerpt from "DNA
Reflex," Submitted by Weyland-Yutani Biological-Weapons Division,
06.08.2185:
"The simple
and efficient elegance of [Internecivus Raptus] is most
likely carried through all aspects of its existence - even down
to the creation of an embryo within a host organism. There are a
great many unknown factors, but extensive research has brought us
to a point that we are confident in the findings and their ability
to be definitively applied to I. raptus.
The creation
of an embryo within a host organism appears to be the direct result
of a deliberate and controlled terminal illness of an extremely
virulent nature. In order for I. raptus to utilize a wide array
of organisms - with a wide array of biological needs and factors
- as host material the simplest, and most logical, course is the
introduction of a viral agent. Viruses are obligate intracellular
parasites. As such they can only reproduce by invading and taking
over other cells because they lack the basic cellular machinery
for self-reproduction. They are comprised of a protein-based capsid
encasing the viral genes and genetic material. Viruses lie somewhere
between living and non-living material. They can reproduce and show
inheritance, but are reliant on the complex enzymes of their hosts,
and in many ways can be treated like ordinary molecules (example:
they can be crystallized). Whether or not they can be classified
as "alive" - they are obligate parasites, and have no
form that can reproduce independent of their host. Like most parasites
they have a specific host range, sometimes specific to one species
(or even limited cell types within a given species) and sometimes
more general. Based on the recorded instances involving I. raptus
activity it is believed that the specific host range for this virus
is that of being "general" with a possible limiting factor
requiring the host to be a eukaryote - specifically of a body mass
of 25 kilograms or greater (It is believed that any organism smaller
than this may result in the premature termination of the host organism
and/or the developing embryo).
It is not uncommon
viral behavior to alter host DNA, or host RNA as well as DNA, in
order to self-replicate. However, this type of behavior dos not
usually create mutations that result in the formation of malignant
growths - such activity is generally the result of transposons when
inserted into host DNA.
Transposons
are naturally occurring sequences of DNA that have the ability relocate
to different positions within the genome of a single cell. In this
process they can cause mutations and change the amount of DNA in
the genome. In order for a transposon to insert itself into a DNA
sequence it requires the enzyme transposase, which is quite often
encoded by the transposon itself. The ends of the transposon sequence
consist of inverted repeats, which are identical sequences reading
in opposite directions. The transposase binds to both the inverted
repeats of the transposon and the target site on the genome. This
target site is cut - leaving the appropriate sticky ends - and the
transposon is integrated and ligated into the target site. Any gaps
that occur are automatically filled in, resulting in direct repeats
within the now restructured DNA sequence.
 By
their very nature transposons are mutagens, and their incorporation
into host DNA are known to cause: altered protein expression in
modified DNA sequences which results in the creation of new and/or
mutated genes; specific genes to stop functioning; improper gap
re-sequencing once relocated to a new position; and the occurrence
of multiple copies of the same sequence can hinder precise chromosomal
pairing during mitosis, resulting in unequal crossovers (one of
the primary causes of chromosome duplication). Generally, transposons
are considered to be parasites that live within the genome of cellular
organisms. In this way, they are similar to viruses. Viruses and
transposons also share features in their genome structure and biochemical
abilities, which have lead to a long-standing speculation that they
share a common ancestor.
It is there
for proposed that the DNA sequence at the center of the virus, as
introduced into a host organism via Stage I. raptus, consists largely
of transposons, which are designed specifically to code for the
creation of a very specific mutation. This mutation causes the malignant
embryonic growth of a Stage 2 I. raptus. It is also proposed that
this growth begins as a small dysplasia in the mediastinum (Dysplasia
is defined as an abnormal form of excessive cell proliferation characterized
by loss of normal tissue arrangement and cell structure. Often such
cells revert back to normal behavior, but occasionally, they gradually
become malignant). As the cells within the dysplasia begin to restructure
and move towards becoming malignant two processes occur: the cells
begin to undergo the process of cellular specialization and further
mitosis; and the forming mass also begins to acquire fatty tissue
from the surrounding area. Thus, creating the initial stage of development
in an I. raptus embryo."
The presentation
of this theory resulted in an increased interest in the Alien, as well
as it's genetic abilities. Even after this theory became the excepted
process there still remained the unanswered question as to how the Alien
is able to retain so much of it's genetic relatedness to other members
of the species through the utilization of transposons. In theory this
type of procreation would only supply the alien with moderate amounts
of I. raptus genetic material. Yet regardless of the generation
the Alien always remains intrinsically "Alien," which may
indicate that I. raptus employs a surprisingly simple genetic
structure enabling vast amounts of coding for its genotype to be held
with in small potions of DNA.
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