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: '''How much human DNA builds our body?''' | : '''How much human DNA builds our body?''' | ||
: Incorporation of genetic material happened more than once. When the human genome was [[wikipedia:DNA_sequencing|sequenced]] on a [[wikipedia:Human_Genome_Project|great scale]], only 1.4% has been found out to encode our ''building material'' - the proteins - the rest appeared to be "junk" DNA. Today we know that 8.5% are old retroviruses (HERVs). -- This brings Agent Smith from the movie Matrix into mind when he [http://www.youtube.com/watch?v=-Na9-jV_OJI classified humans as a virus] because of certain similarities: according to him humans replicated unchecked, consume all resources, and spread to a new area (host) when one area ran out of resources. Now he would have a genetic proof you might think: our DNA is more "virus" than "human". -- Well, the old retroviruses are almost all defective so they don't matter much. Also, noncoding RNA and regulatory sequences - ''tools'' and ''building instructions'' - have been identified from the junk by now. So, yes, no need to panic, we can | : Incorporation of genetic material happened more than once. When the human genome was [[wikipedia:DNA_sequencing|sequenced]] on a [[wikipedia:Human_Genome_Project|great scale]], only 1.4% has been found out to encode our ''building material'' - the proteins - the rest appeared to be "junk" DNA. Today we know that 8.5% are old retroviruses (HERVs). -- This brings Agent Smith from the movie Matrix into mind when he [http://www.youtube.com/watch?v=-Na9-jV_OJI classified humans as a virus] because of certain similarities: according to him humans replicated unchecked, consume all resources, and spread to a new area (host) when one area ran out of resources. Now he would have a genetic proof you might think: our DNA is more "virus" than "human". -- Well, the old retroviruses are almost all defective so they don't matter much. Also, noncoding but function holding RNA and regulatory sequences - ''tools'' and ''building instructions'' - have been identified from the junk by now. So, yes, no need to panic, we can have a calm sleep tonight. | ||
Revision as of 13:38, 30 December 2010
Daodan Chrysalis
Explanation attempt of the biological dimension
Thus the type of damage becomes analyzed and therefore the Daodan requires a sensor system. In nature, “higher lifeforms” evolved by following – among other concepts – specialization and socialization. Those find their expression on one hand in different cell types – therefore multicellular organism – and on other hand in all kinds of symbiosis. So, for a hyperevolved organism, it wound be understandable if it work more intensely by those concepts. A body realizes damage or harmful influences by stimuli. To detect all kind of stimuli, much space is surely needed. Ninety percent of cells that can be found on and inside the human body aren't his own but microorganisms. Fortunately they weigh only a half up to one kilogram. Their assemblage is known as human flora. Depending on the organism, one of them can be a squatter (in metaphorical sense) against real health threatening germs or another one can hold an actual ability like vitamin K production. Some abilities can't be simply or sufficiently integrated into an organism but the ability or its product can be received from a symbiont. So, it seems likely to enlist microorganisms for more sensory tasks and abilities which are actually alien to the human. For this reason, the Daodan needs to upgrade the microorganisms' genomes as well. Their totality is called microbiome. Next, communication between the symbionts has to be ensured. A more or less standardized cell organelle might do the job by using messenger substances. Or it transmits different electromagnetic waves which existence doesn't seem too alien in comparison to the real bioelectric field of each living organism and wound give an explanation attempt of the Daodan glow. (Some metabolic waste products – which are released through the body surface together with perspiration – might become stimulated to glow by the field.) For processing the received information, the Daodan might use an own “self-awareness”, mainly a kind of "bodyimage" formed by another organelle type inside every daodanized cell. The presence of such organelle in neurons opens the possibility for – how geyser coined it – “schizophrenia of the 3rd kind” but also Kerr's idea of a mental interface which allows influence on the Daodan's development by the host's personality. If we want to know more about the decision making algorithms (and their physical structures) which calculates the mutations, we will need to ask Hasegawa. ;-) Depending on the target – human Daodan genome, Daodan microbiome, both their epigenomes, or even organelle genomes (like mitochondrions and plastids have) – a few different “vectors” (e.g. viruses) need to be available to transport the mutation. (To ease further talk one might like to merge the genome names under one term like Daodan metagenome or even shorter daogenome.) However, it's hard to believe that the Daodan could be able to come up with fitting mutations completely by its own. It seems more likely to me that it draws on “genetic building blocks” holding basis information for fast regeneration, resistances, different metabolisms, and so on. Muro and Mai got implanted with prototypes, indeed, but after more than 15 years I think the Syndicate accomplished to developed a Daodan allowing its mass production. This second generation would be independent from the host's sex (XX / YX chromosomes) and metagenome's composition by providing level-zero stem cells. These can target any compatible symbiont cell and then do a “configuration” (whereby they dissolve the unnecessary genetic material) to become classic stem cells and microbes. <div class="NavFrame collapsed" style="width:
Also wird die Art des Schadens analysiert und somit benötigt die Daodan auch ein sensorisches System. In der Natur entstand „höheres Leben“ – unter anderen Konzepten – Spezialisierung und Sozialisierung folgend. Sie finden Ausdruck einerseits in verschiedenen Zelltypen – daher mehrzelligen Organismen – und andererseits in den unterschiedlichsten Symbioseformen. Für einen hyperentwickelten Organismus ist es daher vorstellbar, dass er diese Konzepte verstärkt umsetzt. Der Körper nimmt Schaden oder schädliche Einflüsse durch Reize wahr. Um alle Reizarten detektieren zu können, ist sicherlich viel Platz nötig. Neunzig Prozent aller Zellen, die man an und im menschlichen Körper finden kann, sind nicht seine eigenen aber die von Mikroorganismen. Diese werden in ihrer Gesamtheit Normalflora genannt. Abhängig vom jeweiligen Mikroorganismus kann er beispielsweise „Platzbesetzer“ gegenüber einem wirklich schädlichen Keim sein oder er kann ein echte Fähigkeit haben wie die Produktion von Vitamin K. Manche Fähigkeiten lassen sich nicht so einfach oder nur unzureichend in einen Organismus integrieren. Die Fähigkeit oder ihr Produkt kann aber durch einen Symbiosepartner geliefert werden. Es ist also naheliegend die Mikroorganismen für weitere Sensorik und eigentlich humanfremde Fähigkeiten heranzuziehen. Aus diesem Grund muss die Daodan auch die Genome der Mikroorganismen, zusammengefasst Mikrobiom genannt, aufrüsten. Als nächstes muss Kommunikation zwischen den Symbiosepartner sichergestellt werden. Ein mehr oder weniger standardisiertes Zellorganell in jeder Daodanzelle könnte vielleicht über Botenstoffe dem Rechnung tragen. Oder es sendet verschiedene elektromagnetische Wellen aus, deren Existenz gegenüber dem bioelektrischen Feld eines jeden lebenden Organismus als nicht zu weit hergeholt erscheinen mag und ein Erklärungsansatz für die Daodan-Aura bieten würde. (Einige Stoffwechselabfallprodukte, die über die Haut mit dem Schweiß abgegeben werden, könnten in dem Feld zum leuchten angeregt werden.) Bei der Verarbeitung der Informationen könnte sich die Daodan einem eigenen „Selbstbewusstsein“ bedienen. Dies wäre zum großem Teil eine Art Körperschema, welches sich durch einen weiteren Zellorganelltyp manifestiert. Die Präsenz dieses zweiten Organells in Neuronen ließe die Möglichkeit einer – wie geyser es nannte - „Schizophrenie der 3ten Art“ zu aber auch Kerr's Idee einer mentalen Schnittstelle und somit Einflussnahme auf die Entwicklung der Daodan durch die Persönlichkeit des menschlichen Wirts. Für die genauen Entscheidungsalgorithmen und ihrer physischen Strukturen zur Mutationsfindung müssten wir wohl Hasegawa fragen. ;-) Abhängig vom Ziel – menschliches Daodan-Genom, Daodan-Mikrobiom, ihrer beider Epigenome, oder sogar Organell-Genome (wie Mitochondrien und Plastiden sie haben) – müssen ein paar unterschiedliche „Vektoren“ (unter anderem Viren) verfügbar sein um die Mutation zu transportieren. (Um Diskussionen zu vereinfachen, mag man vielleicht die Gesamtheit der involvierten Genome unter einem Begriff zusammenfassen wie Daodan-Metagenom oder kurz Daogenom.) Trotzdem ist es schwer zu glauben, dass die Daodan vollkommen alleine im Stande wäre passende Mutationen zu erzeugen. Es ist vielleicht glaubwürdiger, wenn die Daodan auf „genetische Bausteine“ zurückgreift, die Basisinformationen für schnelle Regeneration, Resistenzen, unterschiedliche Stoffwechsel, und so weiter enthalten. Muro und Mai wurden Prototypen implantiert, richtig, aber nach mehr als 15 Jahren glaube ich, dass das Syndikat es schafft eine Daodan für die Massenproduktion zu entwickeln. Diese zweite Generation würde durch sogenannte Level-Null-Stammzellen unabhängig vom Geschlecht des Wirts und der Zusammensetzung des mikrobischen Metagenoms sein. Diese Zellen würden jede kompatible Symbiontenzelle zum Ziel haben und nach einer „Konfiguration“ (in welcher sie überflüssiges genetisches Material auflösen) zu klassischen Stammzellen und Mikroben werden."> |
Natural reproduction of human hosts
At new environmental conditions, randomly evolved traits helps members of a population to survive. The survivors then ensure the population's continuity by their reproduction. The Daodan reacts directly on environmental influences and probably – or largely – doesn't know anymore randomness. Therefor it's uncertain if the Daodan can manage or allow random recombination of genetic material during the sexual reproduction of Daodan hosts. For the Daodan, there's actually no more necessity for recombination. So, if no recombination happens, female gamete (egg cells) might become produced with or without genetic material whereby only empty egg cell can accept a male gamete. In any case, the chromosome set is already diploid which means that baby is a genetic clone of one of it's parents. (But you know, the personality is still shaped to a major degree by environment and education.) Contact of male hormones with female gamete (cell nucleus must be presented) marks the cell as fertilized. Implantation and embryonic development follows. The passing on of microbial Daodan symbionts happens during child's birth (...) and by intake of breast milk. (Bifidobacteria can be taken as kind of RL example). <div class="NavFrame collapsed" style="width:
Zufällig hervorgebrachte Merkmale helfen Mitglieder einer Population bei neuen Umweltbedingungen zu überleben. Die Überlebenden sichern den Fortbestand der Population. Die Daodan reagiert direkt auf Umwelteinflüsse und kennt wahrscheinlich – oder zum großen Teil – keine Zufälligkeiten mehr. Bei der sexuellen Fortpflanzung von Daodan-Trägern ist es daher ungewiss ob die Daodan mit der Rekombination des Erbguts zurechtkommt oder dies zumindest zulässt. Es besteht für die Rekombination eigentlich keine Notwendigkeit mehr. Wenn keine Rekombination stattfindet, könnten vielleicht weibliche Gameten (Eizellen) mit und ohne Erbgut entstehen, wobei nur die weibliche Gameten ohne Erbgut ein männlichen Gamet aufnehmen. Die Gameten sind also zu Beginn schon diploid. (Sie haben einen doppelten Chromosomensatz, der für gesunde Menschen erforderlich ist). Der Kontakt von männlichen Hormonen qualifiziert die Eizelle zur „Zygote“; es hat also jetzt den Status „befruchtet“. Nidation und embryonelle Entwickung folgt. Die Weitergabe mikrobiellen Daodan-Symbionten findet bei der Geburt statt (...) und mit der Aufnahme in der Muttermilch. (Die Weitergabe von Bifidobakterien könnte man als eine Art Beispiel aus dem echten Leben nennen.)"> |
Multiple Imago stages
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Static metamorphosis
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Contamination of the ecosystem
GV's "Chrysalis" work group thinks that the Daodan will contaminate the environment sooner or later (in case it didn't already happen) because of horizontal gene transfer causing unseen threats. Hence the Daodan needs a patch. The idea was and is to protect the primer symbiont, the human host. To ensure that the microbial Daodan cells stays only at the human flora these cells need to die in absent of the primer symbiont by dissolving their genetic material with an enhanced degradosome. (Will Pandora hunt down all hosts with an original Daodan (to patch them or kill the hosts) ?) This patch solves only one part of the problem. Existing Daodans would be still a permanent danger, especially the unknown number in Syndicate 'property'. In worst case this threat had to be met on planetary scale. This would require full control over all matter and lifeforms. Silver Village's terraforming research seemed provide first results just in time. Green Village got access to this data and assembled their own prototypes which become slowly adapted to fight the Daodan. (This version of nanobots haven't reached yet their final stage of development.) To give the bots capability for self-awareness they form sensor system and equivalents of neural networks (to create a "body image") whereby some nodes use other artificial organs (for GPS localization, etc). These notes allow humans control over the growth of the bot collective. To prevent the Daodan's continuing contamination and reconquering of already cleaned areas the bots needs to cloak all lifeforms at first, analyzing them, and then killing all separated microbial Daodan cells. This event is code named "silver dawn". Most of the bots will destroy themselves after done work. Only the subterranean nodes will remain giving the possibility to repeat the process in case few Daodans survived. The nanobots have many mechanisms borrowed from living systems and one of its macroscopic appearances is a crystal. Hence GV personal nick named it "bioc". <div class="NavFrame collapsed" style="width: GV's "Chrysalis"-Arbeitsgruppe hält es für wahrscheinlich, dass die Daodan früher oder später (falls dies nicht schon geschehen ist) die Umwelt kontaminiert: horizontaler Gentransfer könnte noch nie gesehende Gefahren entstehen lassen. Deshalb benötigt die Daodan einen Patch. Die Idee war und ist den Primär-Symbionten, den menschlichen Wirt, zu beschützen. Um sicherzustellen, dass die mikrobischen Daodan-Zellen die Normalflora nicht verlassen, müssen sie in Abwesenheit des Primär-Symbionten absterben wobei ihr genetisches Material durch ein verbessertes Degradosom zerstört wird. (Wird Pandora angeheuert um alle Original-Daodan-Wirte zu patchen oder zu eliminieren?) Der Patch löst nur ein Problem. Die bereits existeirenden Daodan-Wirte sind weiterhin einen ständige Bedrohung, besonderst die unbekannte Anzahl an Wirten des Syndikats. Im schlimmsten Fall muss die Gefahr auf planetarer Ebene bekämpft werden. Dies würde aber volle Kontrolle über alle Organismen und Materie voraussetzen. Silver Village's Terraforming-Forschung schien brauchbare Resultat gerade rechtzeitig zu liefern. Green Village erhielt Zugang zu diesen Daten und baute seine eigenen Prototypen. Diese werden langsam dahingehen angepasst die Daodan bekämpfen zu können. (Diese Art von Nanobots ist noch immer in der Entwicklung.) Um den Bots Selbstwahrnehmung zu ermöglichen, wurden sie programmiert Sensoren und Äquivalente neuronaler Netze zu bilden. Dabei gibt es einige Knotenpunkte, die über zusätzliche künstliche Organe verfügen (für GPS-Lokalisierung, etc). Die Knoten erlauben den Menschen Kontrolle über das Wachstum des Botkollektivs. Um die fortschreitende Kontamination und die Rückeroberung bereits gesäuberter Gebiete durch die Daodan zu verhindern, müssen die Bots zunächst alles Organismen einhüllen, sie analysieren und die separierten Daodan-Zellen schließlich vernichten. Die meisten Bots werden nach getaner Arbeit zerstört. Nur die Unterirdischen Knoten werden zurückbleiben, als Absicherung den Prozess schnell zu wiederholen falls doch ein paar Daodan-Zellen überlebt haben. Die Nanobots haben viele Mechanismen aus der Natur kopiert, und eins ihrer makroskopischen Erscheinungsformen ist ein Kristall. Darum gaben die GV-Forscher den Bots den Spitznamen "Biok"."> |
Future upgrades
I don't think this will happen in RS but later sequels. It's better to write it down than forgetting it again during time.
- telomere regeneration: which allows biological immortality (overpopulation problem appears)
- cyborg genes: construction genes which takes care of implants -- nothing special in comparison to our human growth genes -> Omega-Chimäre
- memory chromosome: nanoscanner collect position and properties of neurons and other relevant stuff and code these information into a new chromosome
Omega-Chimäre
- Omega-Chimäres can make use of external memory storage for different Imago stages and also knowledge.
- Long-range objective is to create a collective consciousness (via network) called Daimon.
Symbiosis
The following subsections are meant to show what real symbiosis is capable of and that it exist between very different species. Therefore those sections display combinations of the so-called kingdoms.
Unfortunately viruses are unranked so far. But in my layman understanding they would form the fourth domain and seventh kingdom of life.
- Are viruses lifeforms?
- The problem is that they are neither really dead nor alive. They are zombies so to say. They do nothing until they infect a suitable host cell and becomes active again. Living things were thought to have always an active metabolism. Then tardigrades have been found out to break that rule with their cryptobiosis ("hidden life"). In that stage their metabolism is almost too low for measures (under 0.01%). After that discovery scientists had the rethink the definition of death. The microbes' state of temporary death became some kind of extreme hibernation, namely cryptobiosis, and some Christians were happy that their religion was the sole promise again for resurrection.
- A virus cannot reproduce itself without a host but that's also true for some endoparasites (parasitic organisms in other organisms). And a virus has no own metabolism but can take over the host's metabolism and organelles. In this view a virus might be a very mean and cleaver bastard but it lives.
- From symbiosis to symbiogesesis.
- So a virus makes the host its own body; the news are that there also exist symbiotic viruses. These have not taken over a host cell but sorta vice versa: they became fully incorporated into the host's genome. Two examples: First, the polydnavirus inside of ichneumonid (parasitic) wasps is only produced when the wasps lay eggs into a caterpillar. The virus helps the wasp eggs to survive inside the caterpillar by affecting the immune system and changing the metabolism in advantages of the wasp eggs. The second example is about us humans (and all animals with a placenta). The retrovirus ERVWE1 in our genome merge placenta cells by its produced protein "syncytin" to create a protection layer. That way the embryo keeps untouched by the mother's immune system. Otherwise it could be discovered as foreign body because of the father's genes. The retrovirus gives us an advantage compared to non-placental mammals.
- The polydnavirus is still reproduced but the second virus gave up its independence to the fullest. They, the host and the virus are rather one new organism instead of two. This process of merging organisms is called symbiogenesis.
- How much human DNA builds our body?
- Incorporation of genetic material happened more than once. When the human genome was sequenced on a great scale, only 1.4% has been found out to encode our building material - the proteins - the rest appeared to be "junk" DNA. Today we know that 8.5% are old retroviruses (HERVs). -- This brings Agent Smith from the movie Matrix into mind when he classified humans as a virus because of certain similarities: according to him humans replicated unchecked, consume all resources, and spread to a new area (host) when one area ran out of resources. Now he would have a genetic proof you might think: our DNA is more "virus" than "human". -- Well, the old retroviruses are almost all defective so they don't matter much. Also, noncoding but function holding RNA and regulatory sequences - tools and building instructions - have been identified from the junk by now. So, yes, no need to panic, we can have a calm sleep tonight.
(to be continued)
Fungus and plant
More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis All plants in natural ecosystems are thought to be symbiotic with mycorrhizal and/or endophytic fungi. Collectively, these fungi express different symbiotic lifestyles ranging from parasitism to mutualism. Analysis of Colletotrichum species indicates that individual isolates can express either parasitic or mutualistic lifestyles depending on the host genotype colonized. The endophyte colonization pattern and lifestyle expression indicate that plants can be discerned as either disease, non-disease, or non-hosts. Fitness benefits conferred by fungi expressing mutualistic lifestyles include biotic and abiotic stress tolerance, growth enhancement, and increased reproductive success. Analysis of plant–endophyte associations in high stress habitats revealed that at least some fungal endophytes confer habitat-specific stress tolerance to host plants. Without the habitat-adapted fungal endophytes, the plants are unable to survive in their native habitats. Moreover, the endophytes have a broad host range encompassing both monocots and eudicots, and confer habitat-specific stress tolerance to both plant groups. source: http://jxb.oxfordjournals.org/cgi/content/abstract/59/5/1109 <div class="NavFrame collapsed" style="width: |
Virus, fungus and plant
A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance A mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. We characterized a virus from this fungus that is involved in the mutualistic interaction. Fungal isolates cured of the virus are unable to confer heat tolerance, but heat tolerance is restored after the virus is reintroduced. The virus-infected fungus confers heat tolerance not only to its native monocot host but also to a eudicot host, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants. source: <div class="NavFrame collapsed" style="width: |