How Life Works - Revision history

Robert.adlington: /* 11. Making and Hacking: Redesigning Life */

2025-12-22T10:32:50Z

11. Making and Hacking: Redesigning Life

← Older revision		Revision as of 10:32, 22 December 2025
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	== 11. Making and Hacking: Redesigning Life ==		== 11. Making and Hacking: Redesigning Life ==

			* Bodies are not fully specified by a blueprint, they emerge as solutions to the rules that govern the production of tissues from cells. Guided by these rules, cells find solutions that work.
			* By studying natural organisms, we are just exploring a tiny corner of the option space of all possible beings.
			* Various new directions:
			** Synthetic morphology, or the creation of Multi-Cellular Engineered Living Systems (MCELSs).
			** Recombinant DNA technology and CRISPR-Cas9
			** Metabolic engineering
			** Synthetic biology
			** Organoids - Organized, artificial conglomerates of cells
			** Chimeric embryos - Which contain cells from more than one type of organism.

	== Epilogue ==		== Epilogue ==

			* Life works at all only in relation to its environment.
			* In transitioning first from prokaryotic to eukaryotic life, then from unicellularity to multicellurarity, and after that to major innovations such as the origin of vertebrates and eventually mammals, evolution was in one sense ramping up the levels of complexity that it created from much the same basic ingredients. But this conventional view overlooks another crucial change.
			** For it became necessary, to support such complexity, for evolution to shift the locus of causation within the organism to higher organizational levels.
			** That in turn demanded the introduction of new ways of handling information, and new kinds of autonomy. Relying only on genetic hardwiring is inadequate to sustain the operation of robust multicellular systems, and I have argued the best way to think about the alternatives is as modes of cognition.
			* To the extent that life becomes more cognitive, it depends less on genes for its actual functioning. You might say that the genes delegate the responsibilities for decisions, maintenance, and behavior to higher-level systems
			* Evolution, it seems, doesn't come up with answers so much as generate flexible problem-solving agents that can rise to new challenges and figure things out on their own.
			* We humans are probably anomalous. One of the attributes that most distinguishes us from other animals is our construction of complex cultures, which rely critically on systems and technologies for passing on information and learning) and thus causal influence - between generations through means other than genes. But all this is really just another way in which life has evolved to free itself from genes through an upward transition of power and authority. We are perhaps the prime example of how cognition does that: our minds are capable of promoting profoundly counteradaptive behavior, such as committing suicide at an early age or choosing celibacy.
			* The anatomy-generating core system is highly conserved in metazoa: it doesn't change much between different species, simply because that would be disastrous. These DNA regions are effectively excluded from the list of targets at which genetic change could generate viable selectable phenotypic variation. They just cannot be tinkered with.

Robert.adlington: /* 10. Troubleshooting: Rethinking Medicine */

2025-12-22T09:38:12Z

10. Troubleshooting: Rethinking Medicine

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 == 10. Troubleshooting: Rethinking Medicine ==
 == 11. Making and Hacking: Redesigning Life ==
 == Epilogue ==

Robert.adlington: /* 9. Agency: How Life Gets Goals and Purpose */

2025-12-21T12:30:40Z

9. Agency: How Life Gets Goals and Purpose

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 == 9. Agency: How Life Gets Goals and Purpose ==
 == 10. Troubleshooting: Rethinking Medicine ==
 == 11. Making and Hacking: Redesigning Life ==
 == Epilogue ==

Robert.adlington: /* 8. Bodies: Uncovering the Pattern */

2025-12-20T13:36:44Z

8. Bodies: Uncovering the Pattern

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 == 8. Bodies: Uncovering the Pattern ==
 == 9. Agency: How Life Gets Goals and Purpose ==
 == 10. Troubleshooting: Rethinking Medicine ==
 == 11. Making and Hacking: Redesigning Life ==
 == Epilogue ==

Robert.adlington: /* 7. Tissues: How to Build, When to Stop */

2025-12-20T11:57:05Z

7. Tissues: How to Build, When to Stop

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 == 7. Tissues: How to Build, When to Stop ==
 == 8. Bodies: Uncovering the Pattern ==
 == 9. Agency: How Life Gets Goals and Purpose ==

Robert.adlington: /* 6. Cells: Decisions, Decisions */

2025-12-19T14:05:41Z

6. Cells: Decisions, Decisions

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 * Cells commit to fates by noticing and assessing what their neighbors are doing. It's like voting with a show of hands: we might sneak a look at how others are voting before deciding which way to go ourselves. And if we're given new information, we might change our mind. As new cells are produced by division in the early embryo "they take care of their own further development, shaping both themselves and their local environments without any further instruction from their parents.
 * Each cell inherits the epigenetically modified genome of its parent cell, in which some genes have been silenced while others are active - but it can incur further epigenetic modification, guided by the signals coming from outside, that change its fate still further. In this way, the development of the organism is a story about progressive cell-fate selection, at each stage of which the cell lineage commits to one path and the others become unavailable to it.
 == 7. Tissues: How to Build, When to Stop ==

Robert.adlington: /* 6. Cells: Decisions, Decisions */

2025-12-19T13:33:24Z

6. Cells: Decisions, Decisions

← Older revision		Revision as of 13:33, 19 December 2025
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	== 6. Cells: Decisions, Decisions ==		== 6. Cells: Decisions, Decisions ==

			* We're not just a homogenous mass of cells.
			* Cells commit to fates by noticing and assessing what their neighbors are doing. It's like voting with a show of hands: we might sneak a look at how others are voting before deciding which way to go ourselves. And if we're given new information, we might change our mind. As new cells are produced by division in the early embryo "they take care of their own further development, shaping both themselves and their local environments without any further instruction from their parents.
			* Each cell inherits the epigenetically modified genome of its parent cell, in which some genes have been silenced while others are active - but it can incur further epigenetic modification, guided by the signals coming from outside, that change its fate still further. In this way, the development of the organism is a story about progressive cell-fate selection, at each stage of which the cell lineage commits to one path and the others become unavailable to it.

	== 7. Tissues: How to Build, When to Stop ==		== 7. Tissues: How to Build, When to Stop ==
	== 8. Bodies: Uncovering the Pattern ==		== 8. Bodies: Uncovering the Pattern ==

Robert.adlington: /* 5. Networks: The Webs That Make Us */

2025-12-19T13:17:54Z

5. Networks: The Webs That Make Us

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 == 5. Networks: The Webs That Make Us ==
 == 6. Cells: Decisions, Decisions ==
 == 7. Tissues: How to Build, When to Stop ==

Robert.adlington: /* 4. Proteins: Structure and Unstructure */

2025-12-18T10:10:18Z

4. Proteins: Structure and Unstructure

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 == 4. Proteins: Structure and Unstructure ==
 == 5. Networks: The Webs That Make Us ==
 == 6. Cells: Decisions, Decisions ==

Robert.adlington: /* 3. RNA and Transcription: Reading the Message */

2025-12-17T16:19:03Z

3. RNA and Transcription: Reading the Message

← Older revision		Revision as of 16:19, 17 December 2025
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	* The genome was meant to be a static blueprint, but it is dynamic and responsive to environmental stresses - more like an organ or an organism in an organism.		* The genome was meant to be a static blueprint, but it is dynamic and responsive to environmental stresses - more like an organ or an organism in an organism.
	* microRNA - Is smaller than normal genes and may regulate regulate up to 60% of our genes as well as targeting other microRNAs (and a single mRNA can be targeted by many mRNAs). mRNAs seem to control embryo development and to control pluripotency is embryonic stem cells		* microRNA - Is smaller than normal genes and may regulate regulate up to 60% of our genes as well as targeting other microRNAs (and a single mRNA can be targeted by many mRNAs). mRNAs seem to control embryo development and to control pluripotency is embryonic stem cells
	* Now that the human genome is mapped, the ENCODE project is identifying which parts of the entire genome are transcribed in the cells of different tissues, characterizing the human transcriptome. The HGP showed that only 2% of our genome consists of protein-encoding genes, and most of the rest was considered "junk", but now it seems that genes as protein-encoders are maybe only a small part of what is going on with our genome.		* Now that the human genome is mapped, the ENCODE project is identifying which parts of the entire genome are transcribed in the cells of different tissues, characterizing the human transcriptome. The HGP showed that only 2% of our genome consists of protein-encoding genes, and most of the rest was considered "junk" (non-coding), but now it seems that genes as protein-encoders are maybe only a small part of what is going on with our genome.
			* Encode identified around 37.6k long non-coding RNA (ncRNAs) genes, nearly twice as many as genes that encode proteins.
			* It seems that, for mammals, the noncoding, regulatory regions of the genome are more important than the coding parts. Bacteria have 90% of the genome for protein coding, while we have 2%.
			* Epigenetics (how your behaviors and environment can cause changes that affect the way your genes work) rather blurs the distinction between nature and nurture.
			* Childhood trauma can be correlated with methylation in a person's genome, a biological embedding of experience.
			* The gametes (eggs and sperm) have mechanisms that protect their genomes from much epigenetic alteration, and strip away more or less all of it anyway as these cells mature into the state that takes part in reproduction. At the stage of gamete maturation called the primordial germ cell, epigenetic marks in the genome are largely erased.
			* Rather than waiting for the genome to evolve, it is more effective to evolve mechanisms for producing rapid revisions of how the genes are used when circumstances demand it.
			* Life is according to Dennett and Michael Levin, "cognition all the way down".

	== 4. Proteins: Structure and Unstructure ==		== 4. Proteins: Structure and Unstructure ==