SCP-6009 - 活力組織
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アイテム番号:

SCP-6009

オブジェクトクラス:

TICONDEROGA

main.jpg

ニューロンを取り囲む6009-Catena(2500x)

特別収容プロトコル: SCP-6009の生物学的機能上の必須性のため、現在までに成功した収容プロトコルは存在せず、不可能かつ不要であると考えられています。収容プロトコルは現在、SCP-6009と6009-Catena領域に関する情報漏洩の防止に焦点を当てています。

SCP-6009は微細なサイズであり、異常性が顕著なものではないため、民間の研究者がその異常性を発見する可能性は低いと考えられます。遺伝学、エピジェネティクス、微生物学、神経科学に関する出版物は、SCP-6009に関連する論文が含まれていないかを検査し、出版の可否をナノバイオミクス部門の権限で判断する必要があります。

医学の教科書において、6009-Catena領域は非重要な保護組織として標準化されています。このため、一般の医師や外科医が6009-Catenaの異常性を推測することは不可能だと考えられます。しかし、医学雑誌や脳神経外科の症例報告における6009-CatenaやSCP-6009に関する記述の有無を確認する必要があります。


プロジェクト・ヴィジュネルによって得られた、クラスター連結に関するゲノムデータは、クリアランスレベル3以上の全ての担当者が要求に応じて利用できます。SCP-6009に関する全ての問い合わせおよび試験は、ナノバイオミクス部門の管轄となります。

SCP-6009をTiconderoga1からThaumielに再分類するという提案は、プロジェクト・ヴィジュネルの結果が出るまでの間保留されています。

説明: SCP-6009はヒトのミトコンドリアです。

SCP-6000は構造的にも機能的にも、他の真核生物のミトコンドリアと非常に類似しており、細胞呼吸、細胞周期の制御、および特定のシグナル伝達経路における役割を担っています。SCP-6009は、いくつかの点で非ヒト真核生物のミトコンドリアとは異なります。SCP-6009は、他の真核生物に見られるミトコンドリアとの相違点を複数有しています。

要素 非異常性ミトコンドリア SCP-6009
画像 mito1 mito2
物理的な大きさ ~500-1000 nm ~200-500 nm
運動性 (細胞内) モーター/アダプター複合体(MIRO1)に結合することで運動する。 モーター/アダプター複合体(MIRO1)に結合することで運動する。
運動性 (細胞外) 観察されない。 観察されるが、メカニズムは未解明である。
ミトコンドリアDNA(mtDNA)のサイズ 16000塩基対 16000-18000塩基対
細胞外における存在 血流中に僅かに存在する。 6009-Catenaに関する補遺を参照。
融合と分裂 高頻度 高頻度

補遺 - 6009-Catena: 従来の細胞生物学に反する、SCP-6009の最も顕著な異常性は、6009-Catena領域の存在です。SCP-6009は細胞の外に存在し、コロニー状の構造に集合し、低レベルの運動性を示すことが観察されています。また、SCP-6009は6009-Catena領域で融合して鎖状の構造をとることが観察されますが、同様の挙動は体内の他の場所では観察されません。

6009-Catena領域は、細胞外マトリックスに沿ってSCP-6009の鎖が網の目のように張り巡らされたものであり、脳の神経細胞の樹状突起と有髄軸索の間に織り込まれているのが観察されます。6009-Catena領域のSCP-6009の大部分は大脳基底核を取り囲んでいますが、6009-Catenaの鎖は神経回路の全領域に拡張しています。その質量は白質の約2%ですが、神経機能に何らかの影響を与えていると考えられています。

他の真核生物のものとは異なるSCP-6009の異常性は、6009-Catenaが発見されるまで判明しませんでした。SCP-6009は通常、宿主である人間の死後数時間で消滅するため、死後の検死では6009-Catenaの領域にSCP-6009の活動は検出されませんでした。in vitro培養細胞内のSCP-6009は非異常ミトコンドリアと全く同じ挙動を示すため、長年にわたって研究者はこれを発見することが出来ませんでした。SCP-6009の活動は、6009-Catena領域の神経細胞内および神経細胞外で最も多く見られます。

ChOMP-Seqを用いた、総体的な全ミトコンドリアDNAシーケンシング2により、プロジェクト・ヴィジュネルの焦点となる重要な矛盾が明らかになりました。SCP-6009から発見されたmtDNAの大部分はよく理解されているものであり、通常のミトコンドリア機能の一部であるNADHデヒドロゲナーゼのような非異常タンパク質をコードしています。通常の非異常ミトコンドリアと同様、SCP-6009のタンパク質の多くは核内遺伝子3から合成されています。ヘテロプラスミーはミトコンドリア複製の際の自然な誤りによるものと考えられていましたが、現在ではSCP-6009の機能の鍵となっていると考えられています。未知のミトコンドリア遺伝子の機能と分布が、プロジェクト・ヴィジュネルの研究テーマです。これらの遺伝子は、6009-Catenaの形成に加え、観察された運動性や神経回路への干渉といった他の異常にも関与していると考えられています。

SCP-6009に関連して判明している事実の大部分は、両者ともにナノバイオミクス部門の設立メンバーとして知られる岡見Okami 亮輔Ryōsuke博士(元神経科学部門所属)とChiang 渭火Wei-Huo博士(元遺伝学部門所属)の共同研究によって発見されたものです。

アーカイブ済みプロジェクト申請: 2010/8/29提出(却下); 2010/9/4提出(却下); 2010/9/8提出(却下); 2010/9/20提出(却下); 2010/10/1提出(受理)


他部門との共同研究の申請


申請者 申請者の部門 対象の部門 プロジェクト名
蒋 渭火 遺伝学部門 神経科学部門 -

申請の詳細


SCP-6009のゲノムと6009-Catenaに関する予備調査で、更なる研究が必要であることが示唆されました。今回の共同研究では、以下のことを解明したいと考えています。

1. SCP-6009の運動の理由と方法: SCP-6009は体中を移動することが観察されており、6009-Catenaを形成する方法の鍵となっていますが、細胞外および細胞間の移動方法はよく理解されている細胞内運動に従っていません。

2. 6009-Catenaを形成する理由と方法: ミトコンドリアが細胞機能に果たす役割から、6009-Catenaとそれに囲まれた神経細胞との間には常に相互作用があることは明らかですが、その詳細は分かっていません。また、6009-Catenaの形成過程に何らかのパターンがないか調べることも考えています。

SCP-6009の重要な要素は、6009-Catenaの相互作用、およびその関連性と未知の機能であるため、6009-Catenaとそれが可能な脳との相互作用をよりよくモデル化するために、神経科学の専門知識が必要です。



補遺 - アーカイブ: 以下のやり取りは、プロジェクト・ヴィジュネルによるSCP-6009の初期研究に関連してアーカイブされています。古い情報や不正確な情報が含まれている可能性がある点に留意してください。

2010/10/25

サイト-84
日本、福岡


蒋 渭火 博士

岡見 亮輔と申します。サイト-84のレベル3研究員で、神経科学部門に所属しております。山高管理官より、プロジェクト・ヴィジュネルで貴方と共同研究をするように任命されました。送付頂いたSCP-6009に関する資料と、6009-Catenaの形成に関する仮説を確認しました。

私は長い間、神経科学を研究してきましたが、脳にこのような構造があることは初めて知りました。何千人もの科学者がこのことを見逃していたのか、というのが最初の疑問です。

貴方が部門を超えた共同研究の申請を提出されたのは、神経科学部門が6009-Catenaのモデル構築の助けになると考えられたからでしょうか。従来のMRIやPETスキャンでも、6009-Catenaの大部分が付着している脳の白質をマッピングするのに十分でしたが、何かを修正する必要があったのでしょうか?詳しく教えていただけると助かります。

ご都合の良い時で構いませんので、お短めに返信お願いいたします。Please respond at your briefest convenience.


岡見

2010/10/30

サイト-168
台湾、新竹


岡見博士へ

貴方を仲間に迎えることが出来て非常に嬉しいです。遺伝学部門の私の同僚ですら、SCP-6009プロジェクトにこれほどの信念をを持ってはいません。

私が6009-Catenaを発見したのは全くの偶然でした。私のチームはSCP-3966を研究しており、病気になったばかりの犠牲者から顕微鏡で観察可能な網のような構造を見つけました。私たちはそれがSCP-3966に関連していると考えましたが、SCP-3966とは無関係の死亡したDクラスの広範な検査により、事実が明らかになりました。この構造は非常に小さいため、TEMでしか観察できず、発見するのは困難でした。しかし、どこを見ればいいのかさえ分かれば、ありふれたものでした。

研究室で再現しようとしましたが、なかなかうまくいきませんでした。また、ミトコンドリアは細胞の外では単独で存在しないので、研究は前に進んでいません。

予備実験として撮影した蛍光画像によると、ミトコンドリアは脳の白質全体に広がっており、独自の接続方式を持っています。つまり、いくつかの神経接合部で極小のノードを形成しているのです。私は神経科学については素人で、それが示すところ理解することはできませんでした。

また、この画像によると、キネシンのような通常予想される方法ではなく、自力で体内を移動しています。脳の中をもぞもぞと動き回っていますが、6009-Catenaで最も活発に動いており、ノードの網を形成しています。これを生きている人間で観察することはできませんが、死後数時間以内に何をしているかを知ることはできます。

私は、ヘテロプラスミーが基本的に遺伝子ジャンクと考えられていたために見落とされていた、あまり一般的ではない遺伝子が、運動性に関係しているのではないかと考えています。これは、より荒唐無稽なアイデアに踏み込む前に、まず検証しておくべきことでしょう。

私は現在、その情報を得ることができるシーケンシングプロトコルがないかどうかを調べています。全ゲノムシーケンシングにはそれに近いものがありますが、それだけでは十分ではありません。何か良い案はないでしょうか。

この共同研究に興味がなければ、もちろん断っていただいても構いません。私はこの共同研究の依頼を神経科学部門に何度か出しており、貴方が初めてではありません。網状構造をを最初に発見したジェニー・シェイ博士(同じく神経科学者)でさえ、これ以上調査する価値はないと言っていますが、私は、我々は何かを掴んだのだと思っています。


蒋より

2010/11/20

サイト-84
日本、福岡


蒋 渭火 博士

細胞生物学については素人なので、的外れなことを言っていたとしたら申し訳ないのですが、事前調査報告でおっしゃっていたヘテロプラズムの差異が、SCP-6009から発生する異常である可能性はありますでしょうか?先日読んだ論文では、これまで役に立たないと思われていた、RNAスプライシングの際に除去されるある種のイントロンが、mRNAの分解に関与している可能性があることを最近発見したというものがありました。

そのような方法は可能なのでしょうか?1つのミトコンドリアには何百もの環状DNAのコピーが含まれていますが、その内ごく一部の異常なDNAを考慮するのは、まるで悪夢のような話です。全ゲノム解析ではすでにミトコンドリアDNAが扱われていますが、貴方の新しいアプローチについてお聞きしたいと思っています。

シェイ博士には何度かお会いしたことがありますが、それほど親しくはありません。

共同研究につきましてですが、私は現在他の重要なプロジェクトに取り組んでおりませんので、この提案に興味を持っています。

私は、SCP-6009で多くのことができるとは全く思っていません。まだ少し懐疑的な部分もありますが、共同研究に加わらせていただけると幸いです。このプロジェクトには名前がありますでしょうか?

ご都合の良い時で構いませんので、お短めに返信お願いいたします。


岡見

2010/11/29

サイト-168
台湾、新竹


岡見博士へ

すばらしい気分です!私の秘蔵のプロジェクトを引き受けてくれる人がようやく現れたので、喜びに浸っています。

暗号にちなんで「プロジェクト・ヴィジュネル」と名付けました。- 結局のところ、我々は最後に何が待っているかを知らずにこの謎を解読せんとしているのですから!暗号には興味がありますが、私はコンピュータサイエンスが苦手です。遺伝学は基本的に生物学的な暗号ですからね。

ともかく、脳組織のサンプルから6009-Catenaを見る方法についての情報を添付しておきます。生きている人間ではできませんが、そこは貴方の出番ですね。

何を探しているのかが分かれば、恐らく観察できるはずです。私たちの脳の中にこんな構造があるなんて、今まで誰も気づかなかったでしょうね。

また、私のことは「ウェイリー」と呼んでください。フルネームだと、亡くなった政治家の人の名前に似てるんですよね。


ウェイリー

2010/12/2

サイト-84
日本、福岡


ウェイリーへ

それでは改めて、よろしくお願いします。私のことは「リョウ」とお呼びください。

貴方の成果を辿ってみました。これは非常に注目に値し、非常に繊細なものです。なぜ誰もこれを研究しようとしなかったのでしょうか?これはかなり大きな医学的発見だと思います。

まず、6009-Catena領域のマッピングについてです。従来のMRIやPETスキャンを使えば、SCP-6009が集中して6009-Catenaを形成している場所の大半である、白質をマッピングすることができます。恐らく私は細胞質を除去する方法を見つけることが出来るだろうと思います。そうすれば、マッピングは実行可能になります。

私の同僚のミカエル・アギナルド博士がKhevtuulプローブ計画の初期段階に関与していたので、何らかのアイデアを持っているかもしれません。しかし、SCP-2669のファイルは制限されているので、アギナルド博士は、彼をプロジェクトに参加させる前に、山高管理官に確認して許可を得る必要があると言っています。

最近、ワールド・コネクトーム・プロジェクトThe World Connectome Projectから最新のトラクトグラフィーモデルが発表されましたが、我々の目的には十分な精度ではなく、6009-Catenaの大部分が存在する神経間の空間を見逃しています。私はこの問題についてより深く検討してみようと思います。

そちらのサイトにMRI装置はありますか?うちのはまた壊れてしまったので、毎日電車で大阪まで行っています。サイト-84のことですから、ずっと壊れたままなのではないかという気がします。

ご都合の良い時で構いませんので、お短めに返信お願いいたします。


岡見

2010/12/28

サイト-168
台湾、新竹


リョウへ

素晴らしいですね!アギナルド博士は私たちのチームへの参加を希望しているのでしょうか?

以下は、私がChOMP-Seqと名付けたシーケンス方法の大まかな要約です。この手法は、私たちがSCP-2946のゲノム吸収効果を研究していた際、一度試して上手くいかなかったものに基づいています…まさか有効活用できる日が来ようとは思っていませんでしたね。

見ての通り、これはかなり気の利いたシーケンシング法です。一見上手くいっているように見えますが、並列シークエンスと増幅段階での精査の増加のため、無駄なデータも多くなってしまいます。

そちらのサイトも問題を抱えているようですね…うちは機材については問題ないのですが、Dクラスがたった4人しか割り当てられていません。ChOMP-Seqが実際に機能していることを確認するための予備的な比較や配列の調整を行うために、自分のDNAだけでなく後輩のDNAも採取しなければなりませんでした。

Dクラスの増員要請が通ればいいのですが、無理でしょうね。


ウェイリー

2011/1/5

サイト-84
日本、福岡

ウェイリーへ

なるほど、なかなか賢いやり方ですね。

貴方の優しさに感謝を。ChOMP-Seqというのは、なかなかキャッチーな名前だと思います。しかし、私のイニシャルがそこに含まれることを素直に喜ぶべきかは分かりません…私はちょっとした提案をしただけで、大部分は貴方の仕事が元になっていますし、試験も貴方が行ったものです。

ChOMP-SeqがFASTQやVCF、あるいは単なる.txtファイルのような、より標準的なものを出力する方法はありますか?サイト-84のコンピュータは旧式で、カスタムCSQファイルを変換したり開いたりできないのです。

アギナルド博士は他のプロジェクトも抱えていますが、6009-Catenaのモデル作成には協力してくれるそうです。また、彼は以前の業務の成果を流用する許可を得たそうですから、その点は問題ありません。ドライブにDクラスのCatenaネットワークがいくつか入っているはずですので、必要なものがあるかチェックしてください。各ファイルはサイズが非常に大きいですが、仕方のないことです。スキャンに掛かるのはせいぜい20分程度ですが、その後モデルを生成するとなると、我々のコンピュータは午後までかかってしまいます。勿論、新しいコンピュータさえあれば午後までかかることはないんですがね…

ご都合の良い時で構いませんので、お短めに返信お願いいたします。


岡見

2011/1/20

サイト-168
台湾、新竹


リョウへ

面白い名前や略語を考えるのが、もっぱら私の空き時間の過ごし方です…ちょっと情けないですよね?それに、貴方の名前は母音で始まるので、ネーミングの幅が広がります。ChOMP-Seqは、ランダムな文字の組み合わせよりもはるかにキャッチーですよね。それから、FASTQは恐らく利用可能かと思います。最新版にアップデートしてみてください。

神経マップのファイルを見ました。最初のスキャン後のノード分布を考慮する必要があると思いますが、トラクトグラフィーは私が望むものと全く同じです。

また、責めたりするつもりはありませんが、「お短めにbriefest convenience」は少し変な表現のように思います。「お早めにearliest convenience」という意味でしょうか?


ウェイリー

2011/2/20

サイト-84
日本、福岡


英語は少し苦手なものでして…私は何年も前から、適切で礼儀正しいと思ってそう言ってきました。今まで誰も指摘してくれませんでしたよ…

とにかく、6000-Catenaマッピングを説明するためのスキーマはこのようになりました。これを山高管理官に見せて、プロジェクトに資金を割り当ててもらおうと思っていますが……SCP財団がいかに巨大で強力な組織であるかということを考えると、資金をせしめるのはいつもとても大変なことです。自分が財団の経理担当者だったらと思うとゾッとします。

図は自分で作りました…少し荒いですが、これで要点が伝わると思います。グラフィックチームに送ったので、間に合えばいいのですが。

ChOMP-Seqソフトウェアの新規アップデートで問題が解決されましたが、一体どうやったのですか?貴方はコンピュータは苦手だと言っていませんでしたか?


岡見

2011/2/27

サイト-168
台湾、新竹


いやいや、全くダメといわけではないさ、ある程度のことは分かる。

ええ、バレてしまったようなので白状します。それを直したのはジェニーです。


ウェイリー









2011/3/1

サイト-168
台湾、新竹


リョウへ

山高管理官との打ち合わせはどうでした?

それと、MRIの修理はそんなに面倒ではないでしょう?


ウェイリー

2011/3/7

サイト-84
日本、福岡


ウェイリーへ

やりました。彼は資金配分を決定してくれましたし、実は私のプレゼンに驚くほど注目してくれました。私が手がけたものに、彼がこれほど興味を示したのは初めてです。悪気はないんですが、彼が貴方のプロジェクトを私に任せたのは、それが不発に終わることを予期していたからではないかと疑っていたほどです。

彼はモデルを改良する方法についていくつか指摘してくれました。それと、SCP-6009の運動性や6009-Catenaの形成の原因となるようなシグナル伝達経路に関連する遺伝子について考えているかどうかも聞いてきました。そのような角度から考えたことはありませんでしたよね?シグナル伝達経路はin vitroで観察することができないので、試行錯誤しています。培養しようとすると死んでしまいますからね。ミトコンドリアはバクテリアに由来するのかもしれませんが、実際に機能するためには、細胞質のリボソームと核の遺伝子が必要です。Catena網状構造は、神経細胞との相互作用に間違いなく影響を及ぼしています。


岡見

2011/3/10

サイト-168
台湾、新竹


これは面白いことになりました。というのも、私もジェニーとその話をしていたんです。…彼女は何を研究しているのかは教えてくれませんでしたが、化学経路について同じことを言っていたんです。実は彼女からの提案で、ナノテクノロジー部門との共同研究の依頼を受けました。

彼女はin vivo 神経観察ネクサスというアイデアを思いついたようです。どういう意味かよくわからないけど、すごく面白そうだから乗ってみました。

また連絡します。


ウェイリー

2011/3/25

Site-168
Hsinchu, Taiwan


So, funny story, Ryo. I saw that a "Dr. Matsunaga Yuko" was approved to work with us and thought she's going to work with you but apparently… no, she's here in Taiwan. And apparently she's been at Site-168 for two years now and I've never met her? Interesting, our site isn't that big.

Makes sense since our site is the a nanotech hub, but I just thought it was funny.

We've only been working together for a week and she already made massive improvements on the protein-based probe idea. I've been looking into some chlorosomes antenna complexes from green sulfur bacterium… we'll see where that takes me.

She's amazing at what she does, Ryo. I think you'd love to meet her.


Waley

April 15, 2011

Site-84
Fukuoka, Japan


Waley,

I'm sure I'll see her one day.

I've got some important news: so Yamataka came the other day and said that the Biological Sciences Summit is in Chengdu in like a month, at the beginning of May. He said he wants me to present our work on Project Vigenère, he might be able to get us an hour slot. He wants our teams to meet, so me and Dr. Aguinaldo will be there if you're joining.

I think he just wants us to present the 6000-Catena Hodological Network, but I think you said Matsunaga had promising stuff to show? If we can showcase that then it will truly be impressive.


Okami

April 18, 2012

Site-168
Hsinchu, Taiwan


Oh, that would be wonderful if Director Yamataka could get us a spot, I always wanted to visit Sichuan.

I think the probe-nexus design we have been working on… kind of works? We got a lot of promising results from the D-Class personnel that we've been getting. Matsunaga worked some magic with Site Director Chen and suddenly we have like, 40 of them. Miracle worker, that one.

When I say "kind of works" I mean, it gets us the result we want, but it has a giant drawback, as you can see.

We're trying to improve on the MH nexus design more, but the biggest problem is still signal transduction. The wire is causing all of the problems, since it's basically an open wound in your head and all the D-class complain it's really uncomfortable. It turns there's really no way to easily transmit terabytes worth of data over delicate flesh and bone!

Not a big fan of the acronyms, but since Matsunaga was the hero of the day I'm fine with her getting the naming rights.

You should see the relevant files on our server soon. And yes, we're all going.

You know, we've been collaborating for a few months now, just now it hit me I don't even know what you really look like… I'm sure you look better in person than in that cold Foundation profile picture.

I'm going to give you a big hug when we finally meet, Ryo.


Waley

April 27, 2011

Site-84
Fukuoka, Japan


Waley,

Yamataka looked very shocked.

I will take that as a yes.

See you in Chengdu!


Okami









May 14, 2011

Site-84
Fukuoka, Japan


Waley,

Sorry I was holed up in the convention center all week, spicy food really does a number on me and I didn't want to risk it. Maybe next time I'll join you next time when we're in a city safer for my stomach. Plus I'm not an adventurous spirit in a country I don't speak the language of.. but parts of the old town looked beautiful!

At any rate, while you were on your urban adventure, Yamataka actually brought me and Dr. Matsunaga and introduced us to Dr. Everett Mann.

Dr. Mann was very intrigued by our probe project, and he had a pretty riveting discussion with Matsunaga on probe design and implantation. However, he specifically sought us out to talk about Project Vigenère. He saw our presentation, Waley!

Dr. Mann have taken interest in our project, he thinks what we're doing might lead to something important. He actually has taken up on himself to request the formation of a new department just for this project, and wants us to know if we're willing to do it.

In addition, he said that our mode of collaboration was noble but very inefficient. He said he's honestly impressed we got so far by throwing emails at each other and concurrently working at two underfunded sites: admirable but not efficient at all. Work smarter, not harder, he said. He said it would be better for us if we were at the same site, and he had sent out a notice to some site directors he knew. You might get some offers soon.

There's probably also going to be more people joining us, since we're a going to be a proper department. New departments always get a lot of buzz.

He said that he put in a request for “Department of Mitochondrial Studies” but even a bore like me thinks that is a stupid name. I'm not as creative as you are, can you come up with something punchy?


Okami

June 1, 2012

Site-168
Hsinchu, Taiwan


Oh, wow, that's… a lot to take in at once.

I got a bunch of offers, but the only one that was interesting was from Director Leep Andrews of Site-234, who reached out to me after he heard about our team looking to become a department. He said our work would be great there! His site handles a lot of biological anomalies. He said his site would be perfect for a new budding department. I read over the site dossier; the equipment and facilities available is just so… tantalizing.

I'll give him a heads up if you are willing to move. Is your team ready to move to the US? I know Jenny is thrilled, as we're going to be part of a new department. It's very funny how it could have been me and her being the founding members for all this groundbreaking work from SCP-6000… her loss, I guess!

For our name, how about “Nanobiomics”? Short, simple, punchy, and most importantly, never heard of before - just like our work for Project Vigenère.


Waley

June 8, 2012

Site-84
Fukuoka, Japan

I love it. The site, the name, all of it.

Also, while in China, Dr. Mann asked me if I would be interested in being the department director. Mann warned me about all these responsibilities and hard decisions he had to make… I definitely am not ready yet.

You are far more driven and passionate about the project than I am, and definitely the most brilliant geneticist I've ever seen.

So, salutations and congratulations, Director Chiang!


Okami
























July 29, 2012

Site-234
Alabama


Ryo,

You know, I’m not going to lie, I was kind of mad at you for thrusting the director job at me. I'm not ready for that responsibility either! You could have at least asked first!

But now, I forgive all of that. Pope Waley absolves you of all sin. Go, and sin no more.

I forgive you because Site-234 is… well, everything.

The junior researchers here actually know how to properly operate a PET scan without you yelling at them. The sequencers don't just randomly decide to die without you staring at it every minute. The incubators here don't even have that growth medium smell! I didn't think that was even possible. We got our own labs, Ryo. No more sharing refridgerators, no more of my experiment being ruined because some doofus from Xenobiology cross-contaminated my samples.

Also, Sherry and Leep are so nice! They can't wait to meet you.

This really feels like a reward, man. We've made it.

Back to business: this is what Matsunaga and Jenny have been working on for the past few months. I think Matsunaga said that Dr. Mann had a surprising helpful idea with data overload while they chatted in China. I do not understand nanotechnology at all but I think it works well for one very good reason, as you will see.

So, yeah! No more itchy exit port.

You’ll love it too when you get here, Ryo. Or rather, Assistant Director Okami. (Congratulations, salutations, and all that - can’t expect me to handle everything!) I need someone that is reliable by my side. You aren’t escaping the infamous bureaucracy that infects all parts of the SCP Foundation that easily!

It’s so nice. I feel like our hard work has finally paid off.


Waley

August 9, 2012

Site-84
Fukuoka, Japan


Waley,

I can’t wait to see Site-234! Unfortunately I have to stay behind for another month. Aguinaldo will be there soon though, I’ll get him to bring some of those red bean mochi treats I know you like so much

I have to stay behind because I need to finish the observation of some of the D-Class that I was working on; Dr. Mann was in Japan, and came by Site-84 to chat about our new department. The probe that Matsunaga and Jenny were working on? It was actually on his suggestion that he gave them soon after that last symposium. Jenny finally made a breakthrough with from a new paper on semiconductors that TSMC released, so when they finally came through, Mann wanted to develop a new insertion mechanism with me. We tried some stuff out a week ago, and he finalized his revised procedure. I’m… not especially thrilled about the new procedure, but it’s such a vast improvement over our current one.

As you know, the exit ports for the MH Nexus is the most clunky and error-prone part of an otherwise ingenious product. One, it’s basically an open wound that goes past your meninges. And surgical wounds healing are usually very itchy, so the D-Class would obviously try to scratch it… and well, even though the wire is anchored under the scalp and can’t be removed, pulling on it obviously still affects something.

Mann's tecnhique is… well, just read for yourself.

Mann came up with the OMNI acronym, which was very kind of him, but all I really did was ask a lot of stupid questions when we were testing the technique out. Most of my contribution was the note of concern near the end there.

I've done plenty of intraoperative brain mappings, but never with two endoscopes at once, and since the D-class is awake you can see them stare at you. Not fun for me, but definitely even less fun for the poor dude on the table.

Amnestics obviously mess with your neural mapping and memory formation, and since that's so important to 6000-Catena, not being to use them is really, really unfortunate - maybe that could be another angle of attack in Project Vigenère?

The D-Class obviously hate the surgery, but none of them report the migraines or headaches that were so common from before, and since now there’s no exit port we don’t need to worry about them scratching it. Our psych staff says that there’s no observable behavioral change, which is good news for our study. Allowing them to do other tasks was actually giving us a wider variety of SCP-6000 interactions with the nuclear genome, and also helps since Site-84 has such a limited D-Class quota. They allotted us more people since it's Dr. Mann requesting it, but Site-84 just don't have that much housing space.

I’ll be stuck here for the next month or so before I can go to the US because I need to finish the post-operative observation for them and get some pre- and post- operation 6000-Catena mapping in.

I can’t tell you how much I want to leave this dump of a site. I like Yamataka, but I will not miss tiny little 84.

I look forward to seeing you, and our Nanobiomics family soon.


Okami

August 25, 2012

Site-234
Alabama


Good things come to those who wait. You will love it here, Ryo.

Thanks for the treats! One thing I miss in Alabama is that there’s no good restaurants of any Asian variety anywhere… but the steak here is cheap and delicious, so win some lose some I guess.

I'm glad Mann helped you out with the new implantation… woof, that made me uncomfortable to just read, don't even want to think about it being done.

The probes are important, and the fact that the most irrelevant part is causing the most problems has always annoyed me. I’ve heard it’s itchy as hell around the exit ports, so solving that was nice… this just wasn't quite the solution I thought of.

Anyways, I’m starting a short paper for VGWAS and Chomp-Seq with the association of the 6000-Catena map clustering. I was working on a new method of data analysis, and I met with some of the people that are now in our department to refine the model.

A part of the project I’ve been working on was eliminating statistical noise - one big obstacle in Project Vigenère was that after we filter out the regular genes, there’s really not a lot of useful data left - we are dealing with genes and proteins that exist in extremely minuscule amounts but affect a whole lot.

What do you think? We’ve been finding pretty promising results of certain pathways and genomes - I think the most interesting is that regardless of the D-Class personnel’s race, genetic material, or family history, there always is the high prevalence of mitochondrial DNA that has the MT-A3 gene. Even though most people do have the MT-A3 gene, I only ever see the MT-A3 gene interact with certain chromosomal genes: LRI3, PFO4, CRW2, and a handful of other less common ones.

There’s also certain subclusters that keep popping up - and activate during, say, eating certain foods or doing certain activities. Not sure what's there.

And speaking of D-class, have you tried blindfolding them during the surgery? Wouldn't that also make it less terrifying for them, without seeing two doctors hover over them playing with their brain?


Waley

September 1, 2012

Site-84
Fukuoka, Japan



Waley,

You would think so, but we detect a higher baseline level of stress in all subjects when we tried that. I think it's because not seeing what's happening makes it even scarier… I often feel like I'm obligated to keep apologizing during the procedure. Mann is chill as a cucumber, obviously.

All in all, I'm happy to report though: the OMNI procedure allows full recovery, and definitely should be used instead of our original design.

I’m flying in tomorrow. I am so, so happy we can collaborate in person. No more email chains.


Okami





























April 8, 2013

Site-234
Alabama


Ryo,

I got an unannounced visit from someone representing the Ethics Committee today.

Are you free on the 14th? They want to observe the OMNI Procedure and judge its suitability for use in civilian subjects. Who's also free that day to partner? I think Dr. Aguinaldo is busy that day, so maybe Graham? If you aren’t free, I think Dr. DePaul or Dr. Raskin can do it.

If they approve, we’ll be able to use the Foundation's contacts at the University of Alabama Birmingham as a front to collaborate with other universities and research agencies to get a wider pool for testing.

Which, here's the draft I haven't finished about D-class… I'd probably just throw it to the new people, honestly, I haven't been able to look at the data much because we my schedule is full of interviews.

It's not in the paper but we tentatively named it the D cluster because it's in like, 80% of the D-class data we have, and they have no similar genomic history or background. But the MT-L2 and MT-F5 thing is consistent in almost all of them, which leads to the same UP4 interaction, which results in the same 6000-Catena formation. Very strange if it’s a coincidence, that's why they're currently in the D cluster. It's also usually the more violent ones too, the calmer ones don't seem to have that genetic interaction.

I miss doing research, Ryo. Most of my time now is spent dealing with the logistics of collaborations, approving testing, interviews for people that want to transfer into our department, then meet with Leep and Sherry to discuss equipment upgrade… and hey, we're getting people from other sites interested in being part of Nanobiomics! Ironic, isn't it, since we only came to Alabama to be one team under the same roof…

I'm glad Nanobiomics is popular, and I'm immensely proud of it, but I've been so busy… Project Vigenère is our baby that we don't control anymore, and I am so glad that we've expanded.


Waley

April 12, 2013

Site-234
Alabama



Waley,

No, I didn’t request general public usage, why would I? I do agree that having civilian subjects are going to vastly help expand our scope… at the same time, civilian subjects are usually signing up willingly? So at least it's less fucked up than what we've put these poor D-class through.

I'm free to showcase OMNI, I'll take Graham.

I saw they’ve announced the location for the next Biological Sciences Symposium - May 10 to May 17, and it’s in Kyoto this year! Can you believe it was only last year when we had to beg Yamataka for a measly little spot? Now we’ve been invited to a keynote speaker spot. Just you and me.

I love Kyoto, I’ll show you around. It’s my apology for skipping out in Chengdu.


Okami

April 25, 2013

Site-234
Alabama


Ryo,

Sorry I didn't get back to you sooner, I really need to get some sleep. I forgot about your email, but just now I got a message from EC about the OMNI thing, so, congratulations! I think Leep would be in charge of setting your contracts up.

And yeah! Keynote speakers! I didn't think it would happen in my wildest dreams.

Here's something that might shock their pants off. I've had this in my back pocket for a while now but this is going to give me the kick to finally finish it.

This could be a good update to Project Vigenère. I think it's going to get a lot of people mad because this is a fundamental change of the concept of the "mitochondrial eve", but I think our theory makes the most sense: a particularly robust bacterium, or mitochodria in some ancient human ancestor, and somehow spread to other humans during our early evolution. And seeing how most of the mitochondria's genes needed to be coded by nuclear genomes, wouldn't it make sense for SCP-6000 to similarly affect how mutations worked and in effect drive evolution?

Oh yes, people will get very upset, I can't wait. Just listen to how grandeur "neo-endosymbiosis" feels. I don't think I've even stepped in a lab for a month, much less write a whole paper. I'm going to look into the molecular clock comparisons that Dr. Kirkoff has been working on, don't tell him it's for this.

I want you on this one. Just to be the two of us, a return to basics.



Kyoto sounds lovely.


Waley





















June 1, 2013

Site-234
Alabama


Ryo,

I still can’t thank you enough for planning the Kyoto trip. The symposium was already a smashing success, and that amazing trip was the victory lap that we deserved. We really should do this more often.

Also, on the heels of even more good news: I just got out of a meeting with Leep and Tilda Moose. You’ve heard of her, right? She’s been the long time director of Site-17.

Director Moose has heard our keynote speech about the neo-endosymbiotic theory. She's very intrigued about and says there's a highly classified species that she wants Nanobiomics to look into. It's one of the few extant species that both exhibits near-human intelligence and closely-related evolutionary history. Something Director Moose came across in her early days… she thought that it would be pertinent to the neo-endosymbiotic theory for us to see if a closely related species to us also has SCP-6000 or a similar structure within them.

But that's not why she came to visit in person; she came because she said that the Overwatch Council has taken an interest in our department, and wants us to move our base from Site-234 to Site-17. Here at Site-234 we were mostly dealing with microbiology and biochem stuff, stuff that you can safely keep in a petri dish; but Site-17, well, we’ve all heard the legends about what hides in that place. I don’t even know which ones are true. She says we will know once we accept her offer.

Of course, for our troubles, Director Moose has offered us better compensation, newer machines, higher clearance level, yada yada yada. But most importantly, she says since they’re doing expansions recently, we are getting our own wing in the new building.

I thought Site-234 was swanky, but Site-17… in our own wing… I really don’t know how to respond. I want to get your input as my right hand man, my brother from the start of this wild journey. Leep says he’s really gonna miss us, but, how can I say no?


Waley

June 3, 2013

Site-234
Alabama


Waley,

Site-17? Wow, that’s really not what I was expecting.

I don’t know if we can even afford to say no if the O5 has taken an interest in us.

You’ve always been the one with the big heart. Always being there, not just as one of the most brilliant geneticists I’ve ever seen, but also as a close friend.

Without you I don’t think our department could grow into the powerhouse that it is today. Can we believe we only first met and started Project Vigenere around two and a half years ago? Feels like it’s been my whole life, this wild ride.

We’ve only been here for… eight months? Wow, it feels so much longer than that. I’m gonna really miss Sherry and Leep. At least our department will still all be together. Our weird little family has grown so big now!


Okami

June 8, 2013

Site-234
Alabama


Ryo,

Thank you for the kind words. The same goes for you! Without you we would both be still stuck at our home sites doing god-knows-what…

Also, they’re still building the new wing, but Director Moose has given me clearance for the files we will have access to once we get there. You should have clearance too since you’re Assistant Director. There’s some juicy stuff we can do.

I'm going to be at Site-17 to iron out some paperwork and inspect if the new wing fits in with what we need - I'll be pretty predisposed here since I want to make it a seamless transition, so you might have to take over for a bit.


Waley

June 10, 2013

Site-234
Alabama



I’m reviewing the stuff we have clearance for now. I think SCP-2828 would be of our interest - a vestigal organ that has antimemetic properties? I have some theories about evolutionary techniques that served to protect us from predators having origins in SCP-6000 - after all, we co-evolved, and if the neo-endosymbiotic theory is correct, then this would be one mark for co-evolution.

Remember the SCP-3966 response you worked on that lead to the discovery of SCP-6000? Maybe there's some genomic basis for protection against those 4-dimensional spiders too!

Or why certain people have the genes that develop into SCP-1237 (or, how it developed). Wow, all of these topics that just opened up…

Waley, the Foundation really is a whole treasure trove. I 'm so happy that we took on this wild journey.


Okami

June 18, 2013

Site-234
Alabama



Waley,

I have this early unfinished draft that you should review on a hypothesis regarding reality benders - come to think of it, we never tested on humanoid anomalies. And Site-17 is known for having a ton of them! I've actually never done a brain scan of humanoid SCPs, it's going to be fun trying to map the 6000-Catena and see if the clustering matches up with regular humans!

I've never met a reality bender before, apparently there's some training that we need to do before we are allowed to interact with them. I've already signed up to start by the time we get to Site-17, do you want me to sign you up too?

Sorry, I'm getting ahead of myself.


Okami

July 7, 2013

Site-234
Alabama



Waley,

It's been a few weeks, are you still at Site-17? How does our wing look? I would love to come by but I have to sort through a lot of paperwork for personnel transfer. When did we get more than a hundred people under our department? Also, did you forget you had a job to finish back here? You're not just our director, Waley, you are probably the only person that understands SCP-6000 better than me at this department. We need you as our captain.

Sometimes I feel so lucky that I was assigned to work on Project Vigenere, basically randomly.

We are going to change the world with our project, I can feel it.

We all miss you here at Site-234! Sherry has been asking about you. Where are you?


Okami

July 13, 2013

Site-234
Alabama



Waley,

Someone from the Ethics Committee came by to inform us of guidelines dealing with fetal subjects, because it seems like we will be getting clearance for that now.

This is going to be interesting… I don't imagine the OMNI procedure can be done on fetuses or infants, and I would not subject a baby to that. If we can find a way to make it less traumatizing it could be a great way to finally get confirmation on how 6000-Catena is formed in the first place, before the brain is fully developed!

I really need you back here, collaboration and transfer requests are skyrocketing because someone spread the word about us moving to Site-17.


Okami

July 24, 2013

Site-234
Alabama



Waley,

Director Glass from the Psychology Department came by yesterday looking for you, he says he would really like to initiate a large scale collaboration request. He's been having people looking into the way we are clustering, and he says it's painfully obvious none of us study psychology. So far I've been telling everyone you're predisposed but when they ask me when you'll return, I don't have a good answer.

Are you still inspecting Site-17? It's been like, a month now, how much can there be to sort out?

Please respond at your earliest convenience.


Okami

August 10, 2013

Site-234
Alabama


Waley,

Did you get my last email?

Where are you?


Okami


















































NOTICE FROM THE FOUNDATION RECORDS AND INFORMATION SECURITY ADMINISTRATION


The following files have been flagged by the RAISA database for needing review for the reason Inaccurate Personnel Status

For the reason of Department Director Request, the file(s) selected should be EXPUNGED


September 2, 2013

Site-17
Nevada

Ryo,

I’m sorry I’ve been gone. I was at Site-17 for quite some time, yes, and sorry I kept neglecting your emails. I've read all the them, and I'm glad you're excited! The wing is coming along nicely, and they're giving us stuff I've never even heard of. As for Site-17 itself… walking in the halls, you can sense the secrets hiding behind the walls. It gave me a chilling sort of pride, like you're walking inside history itself.

I… didn't know how to word my thoughts, and I really didn't want to hurt your feelings. The more excited you were the more it hurts for me to think about what I'm about to tell you. You're my closest friend and confidant, so I want you to be the first to know:

I'm planning on resigning as director, and transferring out of our department.

It seems natural since you threw this hot potato of a title at me, I’m throwing it back to you now. Following my transfer, you, as the Assistant Director, would naturally take over as Director of Nanobiomics. I don’t think anyone would complain, everyone loves you at Nanobiomics. Salutations and congratulations, Director Okami!

We really built up this whole department from nothing. You and I, from two underfunded sites, are now growing this project to an unimaginable scale. Even the name "Nanobiomics" commands respect.

I'm really proud of everyone in our department - Jenny, Matsunaga, Michael, even the new people - but I want to thank you specifically, Ryo. I remember like it was yesterday: awkward, overtly formal, only here because you were assigned, and honestly kind of skeptical of our project. The Dr. Okami from three years ago and the Ryo I know now could not be more different. But as the project grew, the creative sparks flew and from the tiny seed grew this behemoth that we stand on. ChOMP-Seq, OMNI, the MH nexus… wow, Project Vigenère really gave us a lot, didn't it? There's people in Nanobiomics working on things I don't even understand anymore.

Despite the grandeur of what we built up for Nanobiomics, SCP-6000 is really, really mundane of an anomaly. Project Vigenère already surpassed its original goals a long time ago. The core anomaly is well understood. We've unknowingly crossed a threshold somewhere.

Director Moose actually showed me this system they were setting up, something that Michael and Matsunaga have been working on. Ostentisibly, it takes in ChOMP-Seq and tries to find the best fit in the clustering data we got from VGWAS, so we can have a pre-projection of how the 6000-Catena region would look like before hodological mapping.

I thought it would be fun to see my own profile. Remember when we were testing early beta versions of ChOMP-Seq and I had to use my own DNA because we ran out of test subjects? That felt like an eternity ago. My genome is still in the Project Vigenère folders so I threw it in just for the sake of it. And I saw the prediction: GPK2/MT-UE4, ABCC11/MT-FR2, O-M122 haplogroup, putting me in the E-8 cluster, the civilian "passionate" and "curious" cluster.

It could be a fluke, since our current cluster labels are about as accurate as a horoscope… but seeing it just pop out on the screen really shocked me. It's only inaccurate because we haven't properly attuned it yet.

I could have checked yours! I respect you too much to do so, but it really disturbed me to even have the opportunity to do that.

I can already envision it: just take a sample, run it through the model, and in a day or two the sleek terminal will pop out your subject's psychological profile and likely decision making. No need to get permission to rack the brains of every poor sap that the Foundation decides to snatch up. And it works best for non-anomalous humans, just everyday folks like us! Well, now we’re going to be at Site-17, we might find out if it actually works on humanoid anomalies. What fun!

And since we have been doing stimulus testing on how 6000-Catena changes neural wiring, Jenny actually sent me plans for the third generation prototype of the MH nexus, which if she was able to create, would be able to affect 6000-Catena directly through a new version of the CMH probe. I don’t think she even realized what she is going to create, and that scared me.

I haven’t been able to sleep since I realized what the endpoint of Project Vigenère is. And every day, I feel watched. I’m suddenly acutely aware of anything I do. It’s like my own mitochondria have betrayed me, which frankly I question my sanity for ever considering that ridiculous idea.

As much as it hurts to think about, I thought about shuttering the department. I have (well, had) the power to make everyone just stop. Ban all research, bury our data, dismantle the department, and we all go back to our old lives. Forget this all happened, another project lost to the Foundation’s annals of time. Maybe even throw this to some MTF with a webcrawler to ensure no civilian ever gets close to the truth either. I actually sent a letter to the Overwatch Council recommending this line of action, but they didn’t get back to me, and I suspect they weren’t big fans of that letter.

I am foolish, Ryo. I really should have seen this sooner. Why have all these higher-ups taken such a keen interest in our project? Moose, Mann, Andrews, Yamataka… It’s not for the betterment of science out of the pure kindness of their hearts, that I can tell you. I don't think they have malicious intent as individuals… but I can't say the same about

Perhaps I'm overthinking it. There are so, so many hurdles to overcome. Maybe we already hit the wall of what we can decipher, and the broadest strokes are the extent. Or maybe I’m just paranoid about nothing, inflating the importance of our department, and ultimately nothing earth-shattering will come of Project Vigenère.

It's not perfect yet, but it's serviceable enough for me to be worried. I'm going to tentatively call my position "genetic determinism" - a person having certain types of genomic interaction can be categorized into certain cluster of behaviors

I mean, I tried to convince myself that's not true. C'mon, our brains don't stay the same our whole lives, that's Neuroscience 101. You're not just… born with what you're going to be like. The outside world changes you. Nature vs Nurture!

I keep telling myself, there's no possible way that the intricacies of the human mind could be broken down into numbers in a machine like that. But a tiny voice in my head

It’s really kind of funny - do you remember my original proposal before it's even Project Vigenère? I listed two goals: investigate how these pesky mitochondria keep moving out and about, and find out how it’s making this weird web in our brain. Well, we certainly answered that second part, but to this day no one really has a clue about how it moves around on its own, and it really is too unimportant for anyone to care.

You're a stronger man than I am. You have the courage to see Project Vigenère to its end. I have conflicted feelings about this incredibly valuable tool. I'm sure the Foundation will find its use for the betterment of humanity. I don't think anyone involved in our quick ascent ever had malicious intent. But I also know we, as an organization, have had a long litany of sins.

I'm sure a few years down the line, even my current moral quandary would be predicted.

You and I had a beautiful time building up this empire; I hope you will forgive me, and I deeply, deeply appreciate our friendship. The Kyoto trip will forever be one of my most cherished memories.



Thank you for making boring my life a little brighter.



I've led the way to the Promised Land, and I am fine watching from the mountaintops. I don't regret my time at Nanobiomics. But I can't continue down this path.



I hope you will maintain contact, but I would understand if you don’t. Or can’t.

Please stay safe in Site-17, for my sake. Once again, congratulations. And good luck.





Some boxes are better left unopened.



Forever your friend,

Waley Chiang





Correction: Dr. Chiang Wei-Huo is scheduled return to the Nanobiomics Department. At request of the Ethics Committee, Director Okami Ryōsuke has enrolled Dr. Chiang in a mandated amnestic corrective regimen.






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