What is Synthetic Biology? Summary

• Engineering Life: Synthetic biology is the design and construction of new biological systems, or the redesign of existing ones, for useful purposes. It’s like engineering, but with the building blocks of life.
• Beyond Genetic Engineering: It goes beyond simply transferring genes; it involves creating entirely new biological “parts,” “devices,” and “systems.”
• DNA as Code: Synthetic biologists often treat DNA as a programming language, writing new genetic “code” to create organisms with novel functions.
• Standardized Parts: A key goal is to create a library of standardized, interchangeable biological parts (BioBricks) that can be easily combined to create more complex systems.
• Applications: Potential applications are vast, including:
  • Medicine: Designing new drugs, therapies, and diagnostic tools.
  • Materials: Creating new biomaterials with unique properties.
  • Energy: Producing biofuels or other forms of sustainable energy.
  • Environment: Developing organisms to clean up pollution or detect toxins.
  • Computation: Building biological computers.
  • FoodCreating entirely new proteins, flavors or agriculture approach, including those without existing limitations
• Top-Down and Bottom-Up: Synthetic biology combines “top-down” approaches (redesigning existing organisms) and “bottom-up” approaches (building new systems from scratch).
• Minimal Cell Attempt in making the simplest, most reduced/essential building-blocks of living cells.
• Bioelectricity’s Potential Role: While synthetic biology primarily focuses on genetic manipulation, bioelectricity could play a crucial role in controlling and coordinating these synthetic systems. The Anatomical Compiler is a *potential* application, though vastly exceeding/transcending even.
• Ethical Concerns: Like any powerful technology, synthetic biology raises significant ethical questions about safety, accessibility, and potential misuse.
• Beyond building parts/structure. Dr. Levin/etc. represent another major shift/difference on understanding Bio development/process: Bioelectricity represent non “hardware” controls (not exclusively genetics or structural modifications as bioengineering and early generation Synth-bio might). This offers unique, profound, even revolutionary tools, such as:
• Rewriting body/organ configuration *without* changing genetic code!
• Top-down control for processes that would be immensely difficult (computationally, knowledge-requirements and execution-effort perspective!)
• Bioelectrical circuit/tissue exhibits goal/decision attributes, which can and does provide many robust intelligent actions at levels below human level reasoning: That may/might be ideal, crucial for very difficult construction problems such as during morphogenesis.

Engineering with the Building Blocks of Life

Imagine being able to design and build living organisms from scratch, just like engineers design and build bridges or computers. That’s the core idea behind *synthetic biology*. It’s a field that combines biology, engineering, computer science, and other disciplines to create new biological systems, or to redesign existing ones, for useful purposes.

Synthetic biology is often described as “engineering life.” It’s about applying engineering principles – like standardization, modularity, and abstraction – to the complex world of biology.

Beyond Traditional Genetic Engineering

Synthetic biology goes *beyond* traditional genetic engineering. Traditional genetic engineering typically involves transferring a gene from one organism to another (e.g., inserting a human insulin gene into bacteria to produce insulin). Synthetic biology aims to create *entirely new* biological parts, devices, and systems that don’t exist in nature.

DNA as a Programming Language

A key concept in synthetic biology is treating DNA as a kind of programming language. Just as computer programmers write code to create software, synthetic biologists write genetic “code” (sequences of DNA) to create organisms with new functions. This “programming” takes advantage on key biological properties, which includes:

• Information can be digitally coded
• Cells perform as logic components; not just bio materials but with function similar to computational elements
• Chemical molecules in bodies react according to established and designable process (at scale!)

BioBricks: Standardized Biological Parts

One of the major goals of synthetic biology is to create a library of standardized, interchangeable biological parts, often called “BioBricks.” These are like LEGO bricks for biology – they can be easily combined and assembled to create more complex systems. These parts include things such as those affecting biological actions such as start/stop a biological expression/suppresion and regulating production of any molecules, for example. 

A BioBrick is a DNA sequence that encodes a specific biological function (e.g., producing a protein, sensing a chemical, or carrying out a logical operation). These parts are designed to be: The goal include:

• Standardized: They have consistent interfaces, making them easy to combine.
• Modular: They can be easily swapped in and out of systems.
• Characterized: Their behavior is well-understood and predictable.
• These could then provide, through engineering methods, complex, new capabilities.

Top-Down and Bottom-Up Approaches

Synthetic biologists use two main approaches:

• Top-Down: Redesigning existing organisms by modifying their genomes. This is like taking an existing piece of software and rewriting parts of its code. This method involves a goal: For an existing cell/genome to perform certain functions, to have properties with values set/designed as engineer or researchers.
• Bottom-Up: Building new biological systems from scratch, using individual components like DNA, RNA, and proteins. This is like writing a new piece of software from scratch.  This often targets producing “artificial cell” that do specific job such as targeting pathogens (fighting infections). This method has no requirements (though some studies propose, in the future, to design the most minimal biological systems) on how natural or “natural looking” outcomes would appear – this focuses, fundamentally on constructing components, parts, that could serve practical functions.
• Minimal cell Also involves “bottom-up” – but it studies for smallest amount of DNA capable of expressing, maintaining living behaviours (growth, replications/sustainability over multi generations, adapting toward stable functions)

Applications of Synthetic Biology: A World of Possibilities

The potential applications of synthetic biology are vast and varied. Some examples include:

• Medicine:
  • Designing new drugs that are more effective and have fewer side effects.
  • Creating new therapies, such as engineered cells that can target and destroy cancer cells.
  • Developing new diagnostic tools that can detect diseases earlier and more accurately.
• Materials:
  • Creating new biomaterials with unique properties, such as self-healing materials or materials that are stronger than steel. Spider-silk has had long research (prior to gene-editing boom) of its unique lightweight and strong property and engineering toward such material can drastically reduce our metal dependence, which have significant production cost.
  • Designing organisms that can produce valuable chemicals or materials.
• Energy:
  • Producing biofuels from algae or other microorganisms.
  • Developing new ways to capture and store solar energy.
• Environment:
  • Developing organisms that can clean up pollution or break down plastic waste.
  • Creating biosensors that can detect environmental toxins.
• Computing:
  • Building biological computers that can process information using DNA or proteins, with “logic gates” to perform complex behaviours.

Bioelectricity and the Anatomical Compiler: A Potential Partnership

While synthetic biology primarily focuses on *genetic* manipulation (changing the “hardware”), *bioelectricity* could play a crucial role in controlling and coordinating these synthetic systems. The dynamic voltage across tissues is software of life that gives instructions. Think of it like the electricity powering traditional systems and sending commands; without electricity most “computerized systems” become inactive chunks of metal. Here’s how:

• Control systems: The compiler would benefit *significantly* from robust, natural (biological), complex (for error correction), and established information “system” to allow a structure/function target.  For instance, tissue memory found/proposed in research is *ideal* for regenerative purpose because no external (from outside of organism itself) knowledge on what has changed or “where to begin” become relevant; unlike if/when one takes computer programming, and try solving the error within massive systems (by having “blueprint”.) Nature-derived complex error correction behaviour greatly simplify requirements!
• Interface: Gap Junctions and bio-signals represent communication pathway.  If bioengineering projects have large group of cellular behaviours that’s NOT capable of intercommunication – then coordination, memory storage, control systems can be highly problematic to execute or define – since those would become external instead of natural components within bio structures, with error and reliability issues. Bioelecticity represents unique ways to interact among these individual cells (even though, on the design they do NOT look or originate as existing “bio-parts”)
  • Consider Anthrobots (where cells outside traditional body setting begin behaving differently), or cryptic planarian: Where morphogenetic structures change but no genetic nor external “computer instruction” cause them (i.e., some “hidden factors” affect them – that the scientists did NOT initially find/control; and also do NOT exist within typical genome.) Bio-electrical tissue level interaction may and is good explanations for it, particularly if many cells or structures exhibit similar behaviours. 
• Morphogenetic Goal and processes: Unlike many bio-hacks (tinkering on bodies/parts), Bioelectricity discoveries may shift or significantly challenge *assumptions*: Dr. Levin discusses and considers those during events, and writes, many published research papers with collaborators in wide variety of fields such as A.I. and Robotics (e.g. to illustrate new/unique approach on control or agent behaviours for instance; bioelectricity represent another path than, typically, more digital and virtual approach), and on cognitive discussions: Biology isn’t a program: Tissues do “goal based” intelligent, complex activities to pursue (morphology as a primary target; behaviour can also be ‘installed’), just as humans choose *goal* instead of, simply performing/being “programmable parts”!
• New method. Bioelectric patterns/circuits have capabilities *unavailable*, entirely outside of traditional bio engineering and/or “hack” methods such as chemical or simply attaching existing circuits.  An example: two-headed worm experiments at the lab:

  Where planeria (worm), despite genetic, anatomical and biochemical components *unchanged* (cut, or modification) become changed fundamentally! With tissue “instruction set” rewritable for different growth form and patterns – where such *permanent/persistent change* require bio-electrical change; the bioelectric signal overrides many existing assumptions. (Genetic level changes will not be enough for structure – e.g. there are chaotic genetic sequence among wild-planarian populations; two-headed planaria cannot/do-not simply explain by genetic only either.) In experiments, such memory also has stability (which imply goal, resistance toward normal states.)

  • It demonstrates power/significance in new research that studies bioelectricity! It is *instructive*; and *reprogrammable*, representing/providing software or similar control!
• Another unique potential from anatomical research is how cells work together and the cognitive property it enables at scales below a nervous system or animal brain: A fascinating discussion (particularly relevant for areas beyond life science, for example philosophy discussions on self-organization, emergence and multi-scale mind capability), where individual cognitive scope/action “joins” for collective behaviour/decision with emergent property: Which does NOT become simply “large”, i.e., some accumulation – that tissue may take entirely different decision outcome. The implications for medicine or general science extend far: Since even human level decisions involve cognitive action-at-scope that depend/connect in groups of tissue/subprocesses!

By acting together, a real “anatomical compiler” can do things otherwise be extraordinarily more difficult (even impossible!)

The Anatomical Compiler could be used to design and build synthetic biological systems from the top down, specifying the desired form and function, and letting the cells, guided by bioelectric signals, self-organize to create the structure. The power of the new model of thinking, combined with advances, tools from other biological approaches could greatly accelerate this path.

Ethical Considerations: Powerful Tools, Great Responsibility

Synthetic biology, like any powerful technology, raises significant ethical concerns. These include:

• Safety: What are the risks of creating new life forms? Could they escape into the environment and have unintended consequences?
• Accessibility: Who will have access to this technology? Will it be used to benefit everyone, or will it exacerbate existing inequalities?
• Dual Use: Could synthetic biology be used to create bioweapons?
• Moral Status of Synthetic Life: Do synthetic organisms have any moral status? What rights, if any, do they have?

Conclusion: Building the Future of Biology

Synthetic biology is a rapidly advancing field with the potential to revolutionize medicine, materials science, energy production, and many other areas. By combining engineering principles with the power of biology, we are gaining unprecedented control over the building blocks of life. Bioelectricity helps us see this field from a brand new way, where biology itself isn’t fixed-design, but capable of profound adaptation, flexibility and creativity, capable of being targeted through an *information* and cognitive “instruction set” change; it expands beyond what could be made – toward new ideas of growth/regeneration and purpose. However, with this power comes great responsibility. It’s essential that we carefully consider the ethical implications of this technology and proceed with caution and foresight, for us to go from what “is known”, toward what “could and will be”: a vision for more powerful, capable and transformative technology and biological design for the next era of biology, by thinking and acting “in new light!”

什么是合成生物学 (Synthetic Biology)？摘要

• 工程生命： 合成生物学是设计和构建新的生物系统，或重新设计现有的生物系统，以实现有用的目的。这就像工程学，但使用的是生命的构建块。
• 超越基因工程： 它不仅仅是转移基因；它涉及创造全新的生物“部件”、“装置”和“系统”。
• DNA 作为代码： 合成生物学家通常将 DNA 视为一种编程语言，编写新的遗传“代码”来创造具有新功能的生物体。
• 标准化部件： 一个关键目标是创建一个标准化的、可互换的生物部件库 (BioBricks)，这些部件可以很容易地组合起来创建更复杂的系统。
• 应用： 潜在应用非常广泛，包括：
  • 医学： 设计新药物、疗法和诊断工具。
  • 材料： 创造具有独特性能的新型生物材料。
  • 能源： 生产生物燃料或其他形式的可持续能源。
  • 环境： 开发生物体来净化污染或检测毒素。
  • 计算：构建生物计算机.
  • 食物：创造全新的蛋白质、口味或农业方法，包括那些没有现有局限性的。
• 自上而下和自下而上： 合成生物学结合了“自上而下”的方法（重新设计现有的生物体）和“自下而上”的方法（从头开始构建新系统）。
• 最小细胞：尝试制造最简单、最简化/必要的活细胞构建块。
• 生物电的潜在作用： 虽然合成生物学主要关注基因操纵，但生物电可以在控制和协调这些合成系统中发挥关键作用。解剖编译器是一个*潜在*的应用，尽管甚至超越了。
• 伦理考量： 与任何强大的技术一样，合成生物学引发了关于安全性、可及性和潜在滥用的重大伦理问题。
• 超越构建部件/结构。 Levin 博士/等。代表了对生物发育/过程理解的另一个重大转变/差异：生物电代表非“硬件”控制（不仅仅是生物工程和早期合成生物可能存在的基因或结构修饰）。这提供了独特的、深刻的，甚至是革命性的工具，例如：
• 在不改变遗传密码的情况下重写身体/器官配置！
• 对原本极其困难（从计算、知识需求和执行工作的角度来看！）的过程进行自上而下的控制。
• 生物电路/组织表现出目标/决策属性，这可以并且确实在低于人类推理水平的水平上提供了许多强大的智能行为：这可能/可能是非常困难的构建问题（例如在形态发生过程中）的理想选择，至关重要。

用生命的构建块进行工程设计

想象一下能够从头开始设计和构建生物体，就像工程师设计和建造桥梁或计算机一样。这就是*合成生物学*背后的核心思想。这是一个结合了生物学、工程学、计算机科学和其他学科的领域，以创造新的生物系统，或重新设计现有的生物系统，以实现有用的目的。

合成生物学通常被描述为“工程生命”。它是关于将工程原理（如标准化、模块化和抽象化）应用于复杂的生物学世界。

超越传统基因工程

合成生物学*超越*了传统的基因工程。传统的基因工程通常涉及将基因从一种生物体转移到另一种生物体（例如，将人胰岛素基因插入细菌中以产生胰岛素）。合成生物学旨在创造*全新*的、自然界中不存在的生物部件、装置和系统。

DNA 作为一种编程语言

合成生物学中的一个关键概念是将 DNA 视为一种编程语言。正如计算机程序员编写代码来创建软件一样，合成生物学家编写遗传“代码”（DNA 序列）来创造具有新功能的生物体。这种“编程”利用了关键的生物学特性，其中包括：

• 信息可以被数字化编码
• 细胞充当逻辑组件；不仅仅是生物材料，还具有类似于计算元件的功能
• 体内的化学分子根据既定和可设计的过程（大规模！）发生反应。

BioBricks：标准化生物部件

合成生物学的主要目标之一是创建一个标准化的、可互换的生物部件库，通常称为“BioBricks”。这些就像生物学的乐高积木 —— 它们可以很容易地组合和组装以创建更复杂的系统。这些部分包括影响生物行为的东西，例如启动/停止生物表达/抑制和调节任何分子的产生。

BioBrick 是编码特定生物功能的 DNA 序列（例如，产生蛋白质、感测化学物质或执行逻辑运算）。这些部件被设计成：目标包括：

• 标准化： 它们具有一致的接口，易于组合。
• 模块化： 它们可以轻松地换入和换出系统。
• 特征化： 它们的行为是易于理解和可预测的。
• 然后，这些可以通过工程方法提供复杂的、新的能力。

自上而下和自下而上的方法

合成生物学家使用两种主要方法：

• 自上而下： 通过修改现有生物体的基因组来重新设计它们。这就像获取现有的软件并重写其部分代码。此方法涉及一个目标：让现有的细胞/基因组执行某些功能，使其具有按工程师或研究人员设定的值/设计的特性。
• 自下而上： 从头开始构建新的生物系统，使用 DNA、RNA 和蛋白质等单个组件。这就像从头开始编写一个新软件。这种方法通常以生产“人造细胞”为目标，这些细胞可以执行特定的工作，例如靶向病原体（对抗感染）。此方法对天然或“看起来自然”的结果如何出现没有要求（尽管一些研究建议，在未来，设计最少的生物系统）—— 它从根本上专注于构建可以发挥实际功能的组件、部件。
• 最小细胞：还涉及“自下而上”—— 但它研究的是能够表达、维持生命行为（生长、多代复制/可持续性、适应稳定功能）的最少量 DNA。

合成生物学的应用：一个充满可能性的世界

合成生物学的潜在应用非常广泛。一些例子包括：

• 医学：
  • 设计更有效、副作用更少的新药。
  • 创造新的疗法，例如可以靶向和摧毁癌细胞的工程细胞。
  • 开发能够更早、更准确地检测疾病的新诊断工具。
• 材料：
  • 创造具有独特性能的新型生物材料，例如自愈材料或比钢更坚固的材料。在基因编辑热潮之前，蜘蛛丝因其独特的轻质和坚固特性而长期受到研究，并且针对这种材料的工程设计可以大大减少我们对金属的依赖，而金属的生产成本很高。
  • 设计能够产生有价值的化学品或材料的生物体。
• 能源：
  • 从藻类或其他微生物中生产生物燃料。
  • 开发捕获和储存太阳能的新方法。
• 环境：
  • 开发能够清理污染或分解塑料垃圾的生物体。
  • 创建可以检测环境毒素的生物传感器。
• 计算：
  • 构建可以使用 DNA 或蛋白质处理信息的生物计算机，具有执行复杂行为的“逻辑门”。

生物电和解剖编译器：潜在的伙伴关系

虽然合成生物学主要关注*基因*操纵（改变“硬件”），但*生物电*可以在控制和协调这些合成系统中发挥关键作用。组织之间的动态电压是生命的软件，提供指令。可以把它想象成驱动传统系统并发送命令的电力；没有电，大多数“计算机化系统”就会变成不活跃的金属块。以下是如何做到的：

• 控制系统： 编译器将*显著*受益于强大的、自然的（生物的）、复杂的（用于纠错）和已建立的信息“系统”，以允许结构/功能目标。例如，在研究中发现/提出的组织记忆对于再生目的是*理想*的，因为没有外部（来自生物体外部）关于什么发生了变化或“从哪里开始”的知识变得相关；不像当一个人进行计算机编程并尝试解决大型系统中的错误（通过拥有“蓝图”）时。自然衍生的复杂纠错行为大大简化了要求！
• 接口：间隙连接和生物信号代表通讯途径。如果生物工程项目有大量*无法*相互通信的细胞行为 —— 那么协调、记忆存储、控制系统可能很难执行或定义 —— 因为这些将成为外部的，而不是生物结构内的自然组成部分，存在错误和可靠性问题。生物电代表了在这些单个细胞之间相互作用的独特方式（即使在设计上它们看起来不像或起源于现有的“生物部分”）。
  • 考虑一下 Anthrobots（传统身体环境之外的细胞开始表现出不同的行为），或 隐秘的涡虫：形态发生结构发生变化，但没有基因或外部“计算机指令”导致它们（即，一些“隐藏的因素”影响它们 —— 科学家最初没有发现/控制；并且也不存在于典型的基因组中）。生物电组织水平的相互作用可能并且是一个很好的解释，特别是如果许多细胞或结构表现出类似的行为。
• 形态发生目标和过程： 与许多生物黑客（修补身体/部分）不同，生物电的发现可能会改变或显著挑战*假设*：Levin 博士在活动中讨论和考虑这些，并与各领域的合作者撰写了许多已发表的研究论文，如 A.I. 和机器人技术（例如，为了说明控制或代理行为的新/独特方法；生物电代表了另一种路径，而不是通常更数字和虚拟的方法），以及关于认知的讨论：生物学不是一个程序：组织确实“基于目标”的智能、复杂的活动来追求（形态作为主要目标；行为也可以被“安装”），就像人类选择*目标*而不是简单地执行/成为“可编程部分”！
• 新方法。生物电模式/电路具有*无法获得*的能力，完全在传统的生物工程和/或“黑客”方法（如化学或简单地连接现有电路）之外。一个例子：实验室的双头蠕虫实验：

  其中涡虫（蠕虫），尽管基因、解剖和生化成分*未改变*（切割或修饰），却发生了根本性的变化！具有可重写的组织“指令集”，用于不同的生长形式和模式 —— 其中这种*永久/持久的变化*需要生物电变化；生物电信号覆盖了许多现有的假设。（遗传水平的变化不足以改变结构 —— 例如，野生涡虫种群中存在混乱的遗传序列；双头涡虫也不能/不能简单地通过基因来解释。）在实验中，这种记忆也具有稳定性（这意味着目标，抵抗正常状态）。

  • 它展示了研究生物电的新研究的力量/意义！它是*指导性的*；并且*可重新编程*，代表/提供软件或类似的控制！
• 解剖学研究的另一个独特潜力是细胞如何协同工作以及它在低于神经系统或动物大脑的尺度上实现的认知特性： 一个引人入胜的讨论（特别是与生命科学之外的领域相关，例如关于自组织、涌现和多尺度思维能力的哲学讨论），其中个体的认知范围/行动“加入”以实现具有涌现特性的集体行为/决策：这不仅仅是“变大”，即某种积累 —— 组织可能采取完全不同的决策结果。对医学或一般科学的影响是深远的：因为即使是人类层面的决策也涉及依赖/连接在一组组织/子过程中的范围内认知行动！

通过共同行动，一个真正的“解剖编译器”可以做一些原本极其困难（甚至不可能！）的事情

解剖编译器可以用于自上而下地设计和构建合成生物系统，指定所需的形式和功能，并让细胞在生物电信号的引导下自组织以创建结构。新的思维模式的力量，结合其他生物学方法的进步和工具，可以极大地加速这一进程。

伦理考量：强大的工具，重大的责任

合成生物学，像任何强大的技术一样，引发了重大的伦理问题。这些包括：

• 安全性： 创造新生命形式的风险是什么？它们会逃到环境中并产生意想不到的后果吗？
• 可及性： 谁将可以使用这项技术？它会被用来造福每个人，还是会加剧现有的不平等？
• 双重用途： 合成生物学能被用来制造生物武器吗？
• 合成生命的道德地位： 合成生物体具有任何道德地位吗？它们有什么权利（如果有的话）？

结论：构建生物学的未来

合成生物学是一个快速发展的领域，有可能彻底改变医学、材料科学、能源生产和许多其他领域。通过将工程原理与生物学的力量相结合，我们正在获得对生命构建块的前所未有的控制。生物电帮助我们以全新的方式看待这一领域，生物学本身不是固定的设计，而是能够进行深刻的适应、灵活性和创造性，能够通过*信息*和认知“指令集”的变化来成为目标；它超越了可以制造的东西 —— 走向生长/再生和目的的新思想。 然而，伴随着这种力量而来的是重大的责任。我们必须仔细考虑这项技术的伦理影响，并谨慎和有远见地前进，让我们从“已知”走向“可能和将会”：一个更强大、更有能力和变革性技术和生物设计的愿景，通过“以新的视角”思考和行动，迎接生物学的下一个时代！