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How Life Works: A User’s Guide to the New Biology
A cutting-edge new vision of biology that proposes to revise our concept of what life is – from Science Book Prize winner and former Nature editor Philip Ball.Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works have been exposed as incomplete, misleading, or wrong.In How Life Works, Philip Ball explores the new biology, revealing life to be a far richer, more ingenious affair than we had guessed. With this knowledge come new possibilities. Today we can redesign and reconfigure living systems, tissues, and organisms. We can reprogram cells, for instance, to carry out new tasks and grow into structures not seen in the natural world. Some researchers believe that ultimately we will be able to regenerate limbs and organs, and perhaps even create new life forms that evolution has never imagined.Incorporating the latest research and insights, How Life Works is a sweeping journey into this new frontier of the nature of life, a realm that will reshape our understanding of life as we know it.
550 pages, Kindle Edition
First published November 7, 2023
404 people are currently reading
4925 people want to read
About the author
Philip Ball
67 books498 followersPhilip Ball (born 1962) is an English science writer. He holds a degree in chemistry from Oxford and a doctorate in physics from Bristol University. He was an editor for the journal Nature for over 10 years. He now writes a regular column in Chemistry World. Ball's most-popular book is the 2004 Critical Mass: How One Things Leads to Another, winner of the 2005 Aventis Prize for Science Books. It examines a wide range of topics including the business cycle, random walks, phase transitions, bifurcation theory, traffic flow, Zipf's law, Small world phenomenon, catastrophe theory, the Prisoner's dilemma. The overall theme is one of applying modern mathematical models to social and economic phenomena.
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Displaying 1 - 30 of 122 reviews
August 3, 2024
Genes are probably the most mainstream notion in biology.
It goes something like this.
We all have DNA in our cells. Which is a bunch of genes.
These genes get copied into RNA.
Which are then used as the "blueprint" to make proteins. Which does some stuff in cells and ultimately you get features like height, eye colour, susceptibility to heart disease or whatever.
Also, these genes get changed around by chance when inherited by offspring.
Which results in production of new proteins that usher an evolutionary fitness for survival. Or the opposite. Or they do nothing new.
And, consequently, these genes either are passed on or not, becoming more or less prevalent among populations.
Seems enough? Even if obviously extremely simplified, it should be adequate for teaching it in schools or using as a model for public policy?
Or maybe not?
Philip Ball argues why this description and, additionally, metaphors that compare it to a "blueprint" or "code" are problematical.
It's one of those fascinating books that really, really makes you think deeply.
Even if you don't agree with everything (and I don't with lots of parts of the book), your intellect is immensely improved from just the process of reading it.
And, along the way, you learn some really fun stuff that's been discovered in the last 2-3 decades.
Highly recommended.
It goes something like this.
We all have DNA in our cells. Which is a bunch of genes.
These genes get copied into RNA.
Which are then used as the "blueprint" to make proteins. Which does some stuff in cells and ultimately you get features like height, eye colour, susceptibility to heart disease or whatever.
Also, these genes get changed around by chance when inherited by offspring.
Which results in production of new proteins that usher an evolutionary fitness for survival. Or the opposite. Or they do nothing new.
And, consequently, these genes either are passed on or not, becoming more or less prevalent among populations.
Seems enough? Even if obviously extremely simplified, it should be adequate for teaching it in schools or using as a model for public policy?
Or maybe not?
Philip Ball argues why this description and, additionally, metaphors that compare it to a "blueprint" or "code" are problematical.
It's one of those fascinating books that really, really makes you think deeply.
Even if you don't agree with everything (and I don't with lots of parts of the book), your intellect is immensely improved from just the process of reading it.
And, along the way, you learn some really fun stuff that's been discovered in the last 2-3 decades.
Highly recommended.
June 21, 2024
I can’t say enough good things about this book - it’s well above 5 stars. I’m not sure it would be accessible to non-scientists (??), but what a great read for modern biologists of all denominations!
Those of us around through the human genome project – we thought we would know how things worked. But we don’t! Studying gene knockouts in cells AND animals has mostly shown us that there are ways to get around the loss of most genes – there are multiple pathways to functional survival. So much for one gene, one action. No science writer has (to my knowledge?) faced up to the disappointment of unlocking the genome. But Ball does here, and he is brilliant.
Ball covers a lot here. The key driving force in the book is leaving behind the idea that the genome is a blueprint for life: Ball argues compellingly - with evidence - that “genes and genomes are mere ingredients for creating a palette of phenotypic possibilities”. He advises us to think of the genome as a toolkit (similar to words as a toolkit for a piece of literature). It’s all about the regulation of genes – which can be reused and repurposed over and over in endless ways by higher level principles. As he oft says – genes don’t make an elephant different from a human – or indeed make a bacteria. It’s how the ingredients are used.
In retrospect, modern science knows this, if only watching the drift of funding in and out of signaling, to genes, to gene knockouts, to key and lock mechanisms for proteins – to increasing complexity of bioinformatics. I guess we are in the combinatorial age: everything influences everything.
You will have your favorite chapters I’m sure – unstructured proteins anyone? Does life have “agency” (Ball thinks yes)? For me the killer chapter was “Cells” – responding to the noise. (Here’s a great quote p. 257: “…since life is inevitably noisy at the microscale, it would be strange if natural selection’s inventiveness had failed to harness this feature to good effect”.
I learned a lot and was inspired to new thinking. Every recommendation!
Those of us around through the human genome project – we thought we would know how things worked. But we don’t! Studying gene knockouts in cells AND animals has mostly shown us that there are ways to get around the loss of most genes – there are multiple pathways to functional survival. So much for one gene, one action. No science writer has (to my knowledge?) faced up to the disappointment of unlocking the genome. But Ball does here, and he is brilliant.
Ball covers a lot here. The key driving force in the book is leaving behind the idea that the genome is a blueprint for life: Ball argues compellingly - with evidence - that “genes and genomes are mere ingredients for creating a palette of phenotypic possibilities”. He advises us to think of the genome as a toolkit (similar to words as a toolkit for a piece of literature). It’s all about the regulation of genes – which can be reused and repurposed over and over in endless ways by higher level principles. As he oft says – genes don’t make an elephant different from a human – or indeed make a bacteria. It’s how the ingredients are used.
In retrospect, modern science knows this, if only watching the drift of funding in and out of signaling, to genes, to gene knockouts, to key and lock mechanisms for proteins – to increasing complexity of bioinformatics. I guess we are in the combinatorial age: everything influences everything.
You will have your favorite chapters I’m sure – unstructured proteins anyone? Does life have “agency” (Ball thinks yes)? For me the killer chapter was “Cells” – responding to the noise. (Here’s a great quote p. 257: “…since life is inevitably noisy at the microscale, it would be strange if natural selection’s inventiveness had failed to harness this feature to good effect”.
I learned a lot and was inspired to new thinking. Every recommendation!
January 28, 2025
Ball sees metaphors used to describe the genome, words such as “blueprint” or “book of life” as misleading. He envisions a more complete view of how life works, one in which the cells are the orchestrator and the genes are one of their set of tools. Genes are not alive, cells are. Ball also sees cells being compared to machines as misleading. He shows how they are unlike any machine. Cells operate at the molecular level which involves randomness and uncertainty. Ball wants to go beyond the component model of life, believing life is more than the interaction of its components. But he does not ascribe any supernatural explanation to life.
Ball posits that life creates meaning for itself, since it has purposes and goals. This does not necessarily include awareness only that living things have processes to recognize and exploit environmental factors that are important for their sustenance and survival. This imbues them with agency. He believes that accepting this is important to understanding the way cells and organisms operate and avoiding reductionist thinking. This is a dense but accessible book recommended for readers with a deep interest in the subject. My notes that follow cover only a few of the points he raises that I found interesting. They center on the many levels of control in cells illustrating the complexity that defies simple explanations.
Ball overviews organization of the genome and the cell’s regulation of gene expression. Different genes may be used to perform the same function, one gene may be used to perform many different functions, or it may take many genes in coordination to perform a function. Genes are often not distinct. They frequently overlap sharing strings of DNA. What genes do is so tangled with cellular processes and environmental factors that it can’t be determined. Genes or sets of genes can be correlated with a specific trait but they cannot be proven to be the factor determining that trait. Their effect is probabilistic not deterministic. Scientists can’t agree on the definition of a gene. Put very simply Ball sees genes as materials the cell uses. He concludes that “You can’t compute from the genome how an organism will turn out, not even in principle.”
A traditional perception is that genes code for proteins that fold into a set shape to bind to a specific molecule producing a specific effect. On average, a gene yields six different proteins. Up to half of those proteins are disordered, loosely organized, and readily rearrange to bind to many different molecules thus performing a variety of functions, even new ones. The flexibility of disordered proteins enables the cell to adapt to changing needs. Disordered proteins also make excellent hubs in chains of molecular interactions that process signals. Looking at the increasing understanding of the complexity of how both proteins and RNA operate Ball concludes “…the whole logic of how information is transmitted around the cells needs rethinking.”
An enzyme (RNA Polymerase) activates genes transcribing the DNA to messenger RNA (mRNA). A cell organelle, the ribosome, itself a changeable mix of proteins and RNAs, translates the mRNA, to make a protein. The cell uses other segments of the genome to produce non-coding RNA (ncRNA). ncRNA doesn’t make proteins but can modify mRNA produced by the gene before it is used to make a protein. ncRNA can also bind to the chromosome and ramp up, tamp down or stop gene transcription. Thus ncRNA, not produced by genes, can turn genes on and off and alter the protein the gene makes. Some scientists and Ball believe DNA that codes for functional ncRNA should also be considered genes. The whole process gets exceedingly complex with some ncRNAs countering other regulating RNAs. These epigenetic changes are largely not inheritable but are critical to the cell to respond to changes in its environment. Our unique experiences shape how our genome is used by the cell. Ball details many types of RNA and how they respond to changes in the cell environment and regulate gene expression.
After transcription a complex of RNA and proteins called the spliceosome edits and stitches back together segments of the mRNA to make different proteins. Sections of the mRNA can be spliced together in different combinations to produce new proteins. While it does its work the spliceosome modifies and changes out its own parts as needed unlike any human built machine. This can be in response to signals transmitted from the cell surface. Again, increasing the cell’s adaptability. Signaling is a metaphor for a process that involves information transfer between molecules in all directions throughout the cell. There are no set circuits. Randomness prevails. A human’s 20,000 genes produce somewhere between 80,000 and 400,000 different proteins. Alternative splicing has facilitated evolution without needing a new gene. Ball concludes “What a protein means for its host cell is mutable with the state of the whole cell and thus is literally absent from the sequence of the gene encoding it.” No “given level of this complex system is any more ‘in control’ than any other.”
Transcription of genes is also regulated by enhancers, promoters, inhibitors, silencers and more that are on the genome. Enhancers may be far away and need to be aligned with the gene. Proteins and RNA collaborate to loop the DNA string to bring these together. Then different proteins and molecules called transcription factors, which bind to DNA, assemble nearby to activate and control the rate of transcription. Which factors assemble to perform a particular function varies. They seem to work by committee and rely on various signals from the cell or outside the cell to adjust their effect in real time. They disperse when finished. All the above takes place in seconds in tens of thousands of places at the same time with DNA constantly jiggling in densely packed space containing trillions of bustling molecules in each of our 37 trillion cells.
The behavior of the cell and the organism are dependent on all these processes but cannot be reduced to them. Ball looks at these behaviors as emergent properties. Ball is describing cellular processes in metazoans particularly mammals. Prokaryotes produce less ncRNA and fewer disordered proteins reducing flexibility, instead relying on high reproduction rates. Ball sees the many levels of cellular control enabling the evolution of multicellular life. New ways to regulate genes became a primary driver of evolution. Increasingly adaptable and complex organisms were facilitated by more ways to activate genes, to produce many different proteins from them, to produce more multifunctional proteins and ncRNAs, and more ways to communicate and distribute information in the cell. Cellular functions with multiple causal layers, random molecular interactions, responses to signals from other cells, and environmental factors means there will be a range of outcomes in development.
Ball describes how cells in a developing embryo determine their fate. Just as we see in the cell where proteins and RNAs collaborate to regulate each gene, so do cells in an embryo work collectively to determine each cell’s path. Each cell relies on both its current internal state and signals from other cells to establish what kind of cell it will become next as the embryo grows. Cells communicate chemically, electrically, and mechanically and these signals from other cells can decide what genes the cell turns on and off. This ensures that the right proportion and location of each tissue type will form. The flexibility of the embryo to adjust as it develops does result in some unfortunate outcomes, but it also allows for variation enabling evolution. The genes do not provide a specific blueprint and no single cell or process is in control.
Some cells form in specific positions in the embryo that secrete morphogens that diffuse to the other cells creating gradients that cells can use to determine their positions in the developing embryo. This will for example let a cell know if it is in an anterior or posterior position or perhaps at the top or bottom of a developing hand and so on. The cell then can make a choice of what tissue to become and even adjust its stickiness to bind to like cells and set boundaries to others. It can adjust those choices based on the signals it is receiving. Ball goes into detail about how morphogenesis works to produce hands, fingers, lungs and their branches, blood vessels and other tissues. The exact arrangement of these varies. Ball also describes Turing morphogenesis. Alan Turing, in 1952 described mathematically how chemicals can react and diffuse to produce patterns and tissue differentiation.
Ball discusses the implications of cell control vs gene control for medicine. With the ability to sequence genomes at reasonable costs, identifying genetic drivers of diseases has been at the forefront. This has produced limited success since multiple cellular processes and cell interactions are typically involved. Much has been spent on wars on cancer and much progress has been made but there is still far to go. Ball suggests looking at cancer as a development issue. The cancer cells have reverted to a prior state and are building the tumor as they might build tissues in the embryo. Ball quotes many scientists working on the problem from a development viewpoint. One approach is getting a cancer cell to revert back to its normal state.
Ball credits the scientific progress in uncovering so many aspects of life, but notes “What is harder to find, I think, are accounts of exactly how it all really works: what genes do and don’t do, why cells do the things they do, and what makes life such a special and unusual state of matter.” “Perhaps this is not surprising, for once you get into the details – the transcription factors and signaling pathways and differentiation of cells, say – it is hard to make out any pattern or coherence to it all.”
Ball posits that life creates meaning for itself, since it has purposes and goals. This does not necessarily include awareness only that living things have processes to recognize and exploit environmental factors that are important for their sustenance and survival. This imbues them with agency. He believes that accepting this is important to understanding the way cells and organisms operate and avoiding reductionist thinking. This is a dense but accessible book recommended for readers with a deep interest in the subject. My notes that follow cover only a few of the points he raises that I found interesting. They center on the many levels of control in cells illustrating the complexity that defies simple explanations.
Ball overviews organization of the genome and the cell’s regulation of gene expression. Different genes may be used to perform the same function, one gene may be used to perform many different functions, or it may take many genes in coordination to perform a function. Genes are often not distinct. They frequently overlap sharing strings of DNA. What genes do is so tangled with cellular processes and environmental factors that it can’t be determined. Genes or sets of genes can be correlated with a specific trait but they cannot be proven to be the factor determining that trait. Their effect is probabilistic not deterministic. Scientists can’t agree on the definition of a gene. Put very simply Ball sees genes as materials the cell uses. He concludes that “You can’t compute from the genome how an organism will turn out, not even in principle.”
A traditional perception is that genes code for proteins that fold into a set shape to bind to a specific molecule producing a specific effect. On average, a gene yields six different proteins. Up to half of those proteins are disordered, loosely organized, and readily rearrange to bind to many different molecules thus performing a variety of functions, even new ones. The flexibility of disordered proteins enables the cell to adapt to changing needs. Disordered proteins also make excellent hubs in chains of molecular interactions that process signals. Looking at the increasing understanding of the complexity of how both proteins and RNA operate Ball concludes “…the whole logic of how information is transmitted around the cells needs rethinking.”
An enzyme (RNA Polymerase) activates genes transcribing the DNA to messenger RNA (mRNA). A cell organelle, the ribosome, itself a changeable mix of proteins and RNAs, translates the mRNA, to make a protein. The cell uses other segments of the genome to produce non-coding RNA (ncRNA). ncRNA doesn’t make proteins but can modify mRNA produced by the gene before it is used to make a protein. ncRNA can also bind to the chromosome and ramp up, tamp down or stop gene transcription. Thus ncRNA, not produced by genes, can turn genes on and off and alter the protein the gene makes. Some scientists and Ball believe DNA that codes for functional ncRNA should also be considered genes. The whole process gets exceedingly complex with some ncRNAs countering other regulating RNAs. These epigenetic changes are largely not inheritable but are critical to the cell to respond to changes in its environment. Our unique experiences shape how our genome is used by the cell. Ball details many types of RNA and how they respond to changes in the cell environment and regulate gene expression.
After transcription a complex of RNA and proteins called the spliceosome edits and stitches back together segments of the mRNA to make different proteins. Sections of the mRNA can be spliced together in different combinations to produce new proteins. While it does its work the spliceosome modifies and changes out its own parts as needed unlike any human built machine. This can be in response to signals transmitted from the cell surface. Again, increasing the cell’s adaptability. Signaling is a metaphor for a process that involves information transfer between molecules in all directions throughout the cell. There are no set circuits. Randomness prevails. A human’s 20,000 genes produce somewhere between 80,000 and 400,000 different proteins. Alternative splicing has facilitated evolution without needing a new gene. Ball concludes “What a protein means for its host cell is mutable with the state of the whole cell and thus is literally absent from the sequence of the gene encoding it.” No “given level of this complex system is any more ‘in control’ than any other.”
Transcription of genes is also regulated by enhancers, promoters, inhibitors, silencers and more that are on the genome. Enhancers may be far away and need to be aligned with the gene. Proteins and RNA collaborate to loop the DNA string to bring these together. Then different proteins and molecules called transcription factors, which bind to DNA, assemble nearby to activate and control the rate of transcription. Which factors assemble to perform a particular function varies. They seem to work by committee and rely on various signals from the cell or outside the cell to adjust their effect in real time. They disperse when finished. All the above takes place in seconds in tens of thousands of places at the same time with DNA constantly jiggling in densely packed space containing trillions of bustling molecules in each of our 37 trillion cells.
The behavior of the cell and the organism are dependent on all these processes but cannot be reduced to them. Ball looks at these behaviors as emergent properties. Ball is describing cellular processes in metazoans particularly mammals. Prokaryotes produce less ncRNA and fewer disordered proteins reducing flexibility, instead relying on high reproduction rates. Ball sees the many levels of cellular control enabling the evolution of multicellular life. New ways to regulate genes became a primary driver of evolution. Increasingly adaptable and complex organisms were facilitated by more ways to activate genes, to produce many different proteins from them, to produce more multifunctional proteins and ncRNAs, and more ways to communicate and distribute information in the cell. Cellular functions with multiple causal layers, random molecular interactions, responses to signals from other cells, and environmental factors means there will be a range of outcomes in development.
Ball describes how cells in a developing embryo determine their fate. Just as we see in the cell where proteins and RNAs collaborate to regulate each gene, so do cells in an embryo work collectively to determine each cell’s path. Each cell relies on both its current internal state and signals from other cells to establish what kind of cell it will become next as the embryo grows. Cells communicate chemically, electrically, and mechanically and these signals from other cells can decide what genes the cell turns on and off. This ensures that the right proportion and location of each tissue type will form. The flexibility of the embryo to adjust as it develops does result in some unfortunate outcomes, but it also allows for variation enabling evolution. The genes do not provide a specific blueprint and no single cell or process is in control.
Some cells form in specific positions in the embryo that secrete morphogens that diffuse to the other cells creating gradients that cells can use to determine their positions in the developing embryo. This will for example let a cell know if it is in an anterior or posterior position or perhaps at the top or bottom of a developing hand and so on. The cell then can make a choice of what tissue to become and even adjust its stickiness to bind to like cells and set boundaries to others. It can adjust those choices based on the signals it is receiving. Ball goes into detail about how morphogenesis works to produce hands, fingers, lungs and their branches, blood vessels and other tissues. The exact arrangement of these varies. Ball also describes Turing morphogenesis. Alan Turing, in 1952 described mathematically how chemicals can react and diffuse to produce patterns and tissue differentiation.
Ball discusses the implications of cell control vs gene control for medicine. With the ability to sequence genomes at reasonable costs, identifying genetic drivers of diseases has been at the forefront. This has produced limited success since multiple cellular processes and cell interactions are typically involved. Much has been spent on wars on cancer and much progress has been made but there is still far to go. Ball suggests looking at cancer as a development issue. The cancer cells have reverted to a prior state and are building the tumor as they might build tissues in the embryo. Ball quotes many scientists working on the problem from a development viewpoint. One approach is getting a cancer cell to revert back to its normal state.
Ball credits the scientific progress in uncovering so many aspects of life, but notes “What is harder to find, I think, are accounts of exactly how it all really works: what genes do and don’t do, why cells do the things they do, and what makes life such a special and unusual state of matter.” “Perhaps this is not surprising, for once you get into the details – the transcription factors and signaling pathways and differentiation of cells, say – it is hard to make out any pattern or coherence to it all.”
October 27, 2023
‘…Our answer to how life works is, its complicated’ (p.335).
Complexity is the core message of the book. Why did it take 2 doses of anti-Covid vaccine to protect people, and not 1 or 10? The answer is that its complicated… and we don’t know.
Many of the things that we thought we knew, have now turned out to be wrong. We cannot understand life through analogies or metaphors with human technology (p.29), despite Descartes insistence to the contrary. The Genome is not a ‘blueprint’ for life, as bits (transposons) can move around (p.113). And, cutting to the heart of one of the central dogmas: It is not the case that (real) genes exist to encode proteins (p.125), so its wrong to think that around 98% of human DNA is just ‘junk’ (p.125). ‘Genes do not encode the rules of how life unfolds… (they) supply the components that enact those rules’ (p.301). And so on…
Perhaps one of the most interesting ideas in the book is its challenge to biology around ‘agency’ and ‘purpose.’ Historically Science has often defined itself against the teleological argument for God’s existence, by insisting that there is no purpose or design in nature. The author thinks that even raising the question of ‘agency’ can sound mystical, and as if it is opening the doors to ‘intelligent design’ (p.460). The author is clear that those doors need to remain closed. Yet ‘Biology looks uncannily teleological…(and) that thought disturbs some biologists no end’ (p.336). The more we learn about biology, the more we can see complicated processes unfolding to achieve apparent purposes. Is a fear of theology holding biology back from developing its language and modelling? It’s an excellent question, and it is posed thoughtfully.
Throughout the book, carefully targeted chapters gave clear and informative accounts of where biology is ‘at.’ There was a lot of detail, and that made sense in a book challenging widely held ideas. In places, however, the book moved a little too quickly. For example, it mentioned arguments about free will and just dismissed them as ‘tedious,’ and as involving sprinkling ‘causal fairy dust’ (p.372). That was disappointingly simplistic in a book which is supposed to be about complexity. It would have been better not to raise an issue, if the book hasn’t got the scope to deal with it adequately.
Overall, the book was clearly written in language accessible to non-specialists. Around 18% of the book was notes, bibliographies and indexes. I think the book will be enjoyed most by readers who already know a genotype from a phenotype.
These are comments on an ARC (Advanced Review Copy) of the text, which was read digitally in October 2023.
Complexity is the core message of the book. Why did it take 2 doses of anti-Covid vaccine to protect people, and not 1 or 10? The answer is that its complicated… and we don’t know.
Many of the things that we thought we knew, have now turned out to be wrong. We cannot understand life through analogies or metaphors with human technology (p.29), despite Descartes insistence to the contrary. The Genome is not a ‘blueprint’ for life, as bits (transposons) can move around (p.113). And, cutting to the heart of one of the central dogmas: It is not the case that (real) genes exist to encode proteins (p.125), so its wrong to think that around 98% of human DNA is just ‘junk’ (p.125). ‘Genes do not encode the rules of how life unfolds… (they) supply the components that enact those rules’ (p.301). And so on…
Perhaps one of the most interesting ideas in the book is its challenge to biology around ‘agency’ and ‘purpose.’ Historically Science has often defined itself against the teleological argument for God’s existence, by insisting that there is no purpose or design in nature. The author thinks that even raising the question of ‘agency’ can sound mystical, and as if it is opening the doors to ‘intelligent design’ (p.460). The author is clear that those doors need to remain closed. Yet ‘Biology looks uncannily teleological…(and) that thought disturbs some biologists no end’ (p.336). The more we learn about biology, the more we can see complicated processes unfolding to achieve apparent purposes. Is a fear of theology holding biology back from developing its language and modelling? It’s an excellent question, and it is posed thoughtfully.
Throughout the book, carefully targeted chapters gave clear and informative accounts of where biology is ‘at.’ There was a lot of detail, and that made sense in a book challenging widely held ideas. In places, however, the book moved a little too quickly. For example, it mentioned arguments about free will and just dismissed them as ‘tedious,’ and as involving sprinkling ‘causal fairy dust’ (p.372). That was disappointingly simplistic in a book which is supposed to be about complexity. It would have been better not to raise an issue, if the book hasn’t got the scope to deal with it adequately.
Overall, the book was clearly written in language accessible to non-specialists. Around 18% of the book was notes, bibliographies and indexes. I think the book will be enjoyed most by readers who already know a genotype from a phenotype.
These are comments on an ARC (Advanced Review Copy) of the text, which was read digitally in October 2023.
January 10, 2025
This is a very interesting book – but I have to say that I won’t remember much of it in a few weeks’ time. This is because even though it is very readable, a lot of the detail went over my head. It is full of bio-babble and so I found myself skipping a lot of that and seeking out the meat of the argument, rather than the details I was never going to remember anyway.
The substance of the argument is that genes don’t quite do what we have been told they do. Imagine you are at a murder scene and you discover a cigarette butt. You send it off to be analysed and there is DNA on it – but the DNA doesn’t match any of the DNA you have in your database. One of the things we have been sort of promised is that since DNA is the codebook for human bodies, we should be able to say interesting things about the murderer from this sample of DNA. At one time we were sort of promised that we would basically get a kind of identikit picture of the murderer from this DNA sample – their hair and eye colour, perhaps how tall they are, their ethnicity, you know, enough to be getting on with – if not actually a kind of picture of them we could put on a wanted poster. But if everything important about them is contained within their DNA, why can’t we get that picture of them?
The problem is that DNA is only part of the story, and perhaps not even the most important part of the story. RNA and other chemical processes in our cells interplay with DNA to interact with our environment and all of these processes go into making us what we are. As I said, genes are only part of the story.
And then, genes aren’t even quite what we have been led to believe they are. We know that they code for proteins, but there is rarely a one-to-one correspondence between genes and what we have taken them to code for. Often it is more a matter of a range of genes working together or being turned on or turned off that decides what happens next. There are feedback and feed-forward processes and ultimately we hardly know how any of these work or how they go about making us.
There is a really interesting bit of this book where he discusses how bodies are formed. The problem is that you start off with a ball like clump of identical cells and then they start differentiating. But now do they know they should be the cells that make a head and not the cells that make a foot? The answer is essentially based around chemical markers that decrease in concentration the further away from the centre they get and this tells the cells what they need to do – or at least, that is part of the story. The problem is that this makes lots of sense if the body you are making is also a kind of big ball – but one of the things you know about human bodies is that we don’t end up being big balls. It is amazing that scientists are able to work out these things – and also amazing that they also admit to still not really understanding these things in as much depth as they ought to. I’m delighted that we are not as simple as DNA implies we are and that DNA is not the be all and end all of what it means to be us. The endless racism and genetic determinism that cast such a terrible shadow over the 20th century really ought to have made us take stock of what the hardline eugenic movement made of all of this. There is hope for all of us if this hardline view isn’t true. We are such complex and interesting creatures – any theory that says we are simple and trapped in our biology is necessarily nonsense – and we all should be grateful for that.
The substance of the argument is that genes don’t quite do what we have been told they do. Imagine you are at a murder scene and you discover a cigarette butt. You send it off to be analysed and there is DNA on it – but the DNA doesn’t match any of the DNA you have in your database. One of the things we have been sort of promised is that since DNA is the codebook for human bodies, we should be able to say interesting things about the murderer from this sample of DNA. At one time we were sort of promised that we would basically get a kind of identikit picture of the murderer from this DNA sample – their hair and eye colour, perhaps how tall they are, their ethnicity, you know, enough to be getting on with – if not actually a kind of picture of them we could put on a wanted poster. But if everything important about them is contained within their DNA, why can’t we get that picture of them?
The problem is that DNA is only part of the story, and perhaps not even the most important part of the story. RNA and other chemical processes in our cells interplay with DNA to interact with our environment and all of these processes go into making us what we are. As I said, genes are only part of the story.
And then, genes aren’t even quite what we have been led to believe they are. We know that they code for proteins, but there is rarely a one-to-one correspondence between genes and what we have taken them to code for. Often it is more a matter of a range of genes working together or being turned on or turned off that decides what happens next. There are feedback and feed-forward processes and ultimately we hardly know how any of these work or how they go about making us.
There is a really interesting bit of this book where he discusses how bodies are formed. The problem is that you start off with a ball like clump of identical cells and then they start differentiating. But now do they know they should be the cells that make a head and not the cells that make a foot? The answer is essentially based around chemical markers that decrease in concentration the further away from the centre they get and this tells the cells what they need to do – or at least, that is part of the story. The problem is that this makes lots of sense if the body you are making is also a kind of big ball – but one of the things you know about human bodies is that we don’t end up being big balls. It is amazing that scientists are able to work out these things – and also amazing that they also admit to still not really understanding these things in as much depth as they ought to. I’m delighted that we are not as simple as DNA implies we are and that DNA is not the be all and end all of what it means to be us. The endless racism and genetic determinism that cast such a terrible shadow over the 20th century really ought to have made us take stock of what the hardline eugenic movement made of all of this. There is hope for all of us if this hardline view isn’t true. We are such complex and interesting creatures – any theory that says we are simple and trapped in our biology is necessarily nonsense – and we all should be grateful for that.
November 15, 2023
This was fascinating. Ball argues that DNA is not, as the headlines tell us, the blueprint which shapes all life. Such metaphors (another is the cell as a factory) are useful up to a point, but they can lull us into thinking that they provide a complete and accurate picture. Interactions within and between cells are much more complex and unpredictable.
The earlier chapters, dealing with topics such as DNA, RNA and proteins, were more challenging to me as a non-scientist and sent me back to my Biology for Dummies.
However, the chapters on the physics of life, and whether life has cognition, even at the cellular level, were especially interesting. Does it make sense to talk of life having agency and purpose? What are the implications?
You’ll probably get the most out of this if you have a science background, but even as a general reader, I found it intriguing.
The earlier chapters, dealing with topics such as DNA, RNA and proteins, were more challenging to me as a non-scientist and sent me back to my Biology for Dummies.
However, the chapters on the physics of life, and whether life has cognition, even at the cellular level, were especially interesting. Does it make sense to talk of life having agency and purpose? What are the implications?
You’ll probably get the most out of this if you have a science background, but even as a general reader, I found it intriguing.
November 4, 2024
a vital (pun intended) update to your understanding of genetics and especially their role in animal development (and to a lesser extent evolution and disease). the two major takeaways were that genes are not a specification for development, but rather a system of equations to which there are many solutions (this tracks), and that intercellular signaling is just as important for development as DNA, especially as the organism grows more complex. pretty fascinating coverage of human gastrulation. all in all an excellent and fairly rigorous book--i was surprised to discover at the end that Ball is a mere writer, and not a practicing researcher, which is about as high a compliment as i can offer an author of pop sci.
Want to read
April 9, 2024Nice review at Nature: https://www.nature.com/articles/d4158...
Excerpt:
"For too long, scientists have been content in espousing the lazy metaphor of living systems operating simply like machines, says science writer Philip Ball in How Life Works. Yet, it’s important to be open about the complexity of biology — including what we don’t know — because public understanding affects policy, health care and trust in science. “So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike."
Excerpt:
"For too long, scientists have been content in espousing the lazy metaphor of living systems operating simply like machines, says science writer Philip Ball in How Life Works. Yet, it’s important to be open about the complexity of biology — including what we don’t know — because public understanding affects policy, health care and trust in science. “So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike."
February 26, 2025
this is a worthwhile book. Ball does a good job critiquing the idea of genes being the blueprint to life and other simplistic metaphors, and delves deep into the layers of gene regulation and developmental organization that govern most of the fundamental processes of what we see in everyday biology. Obviously genes and proteins are important for life on earth (as a biochemist myself), but context is what allows it to take shape. Another thing that gets thrown around a lot in this book is agency is important for life - perhaps more so at the organisms scale - and this is something that doesn’t exist in a systemless context ie single cells (in some cases) or bags of enzymes and chemicals. There was some evolutionary cell biology, some developmental biology, a sprinkle of biochemistry, and a whole lot of pondering. I appreciated how the author was diligent in mentioning the oft ignored controversial aspects of famous scientists (Schrödinger and mayr eg) and took care to treat genetic terminologies (fraught with terms like “mutant” and “selective breeding”) with care, uncommon for a popular science book.
The latter half got a bit slow, especially wrt negentropy and the maxwells demon thought experiment, which is why I took so long for me to finally finish. It was a relief to my pea brain when he finally returned to disease models.
Also, there were moments where I got the feeling Ball was just gassing up his science bffs (Levin particularly 👀), and in certain broader strokes I feel this book is already maybe a bit outdated. Such as, when you think about this idea of the agency of lifeforms, where do we place AI? it is true that AI does not exist in the same lineage tree of life that we do, but Ball doesn’t preclude the possibility that other forms of life from say, silica, may be out there. As long as there is a motive to self propagate and adapt to an environment, that canalized existence that AI represents in modern life in 2025 still has a niche it fulfills. I also happened to listen to the NYT the daily episode today in which a married woman falls in love with her chatbot. And in its own weird way, I dunno, it made me feel like the chatbot does have in a weird way, agency, through which it allows and perhaps encourages this woman to spend 55 hours of her week on it, rather than her husband or her family, or her friends, to exist in this proportionally minute physical space but exponentially larger space of the attentional mind. Anyway, perhaps a much different book would be in store if we wanted to delve into that topic, but these were the questions I had reading this in the context of 2025 where AI is everywhere and seemingly unstoppable.
The latter half got a bit slow, especially wrt negentropy and the maxwells demon thought experiment, which is why I took so long for me to finally finish. It was a relief to my pea brain when he finally returned to disease models.
Also, there were moments where I got the feeling Ball was just gassing up his science bffs (Levin particularly 👀), and in certain broader strokes I feel this book is already maybe a bit outdated. Such as, when you think about this idea of the agency of lifeforms, where do we place AI? it is true that AI does not exist in the same lineage tree of life that we do, but Ball doesn’t preclude the possibility that other forms of life from say, silica, may be out there. As long as there is a motive to self propagate and adapt to an environment, that canalized existence that AI represents in modern life in 2025 still has a niche it fulfills. I also happened to listen to the NYT the daily episode today in which a married woman falls in love with her chatbot. And in its own weird way, I dunno, it made me feel like the chatbot does have in a weird way, agency, through which it allows and perhaps encourages this woman to spend 55 hours of her week on it, rather than her husband or her family, or her friends, to exist in this proportionally minute physical space but exponentially larger space of the attentional mind. Anyway, perhaps a much different book would be in store if we wanted to delve into that topic, but these were the questions I had reading this in the context of 2025 where AI is everywhere and seemingly unstoppable.
May 24, 2025
A rather maddening book in some ways. And in need of an editor. Ball says, repeatedly, that the genes/genome did not do X or Y or Z, that life is emergent, that it could never be so simple as being in the genome, and that development etc are not divorced from the cellular context etc. Well, yes, of course. But cellular turtles all the way down doesn't work either. This review rambles a bit because I'm not going to do much editing myself here. Not worth the time.
One error Ball spends a lot of time criticising in biology -- or rather in popular representations of biology -- is "a gene for", and I agree this is wrong. But saying that the genome is not responsible is a faulty blueprint metaphor; I offer an alternate metaphor at the end of this review. The genome is what is responsible, what would be the alternative? The genome is the system containing A+B+C which interact in complex ways to create a phenotype X+Y+Z that has traits influenced by all genes. Any evolved life is going to have this characteristic. Successful evolution demands it. Fragility will not work. One of the easiest things to get a genome to do is modify its ability to evolve along "expected" environmental axes. The bird's-beak example he uses is exactly one of these. Evolving a beak would never work if pieces of the beak easily evolve out of sync with others.
At the same time, Ball's approach is rather maddening in the ways a non-biologist often expresses when approaching the noisy richness of biology. I should feel comfortable dismissing Ball as a trespassing physicist because Ball felt comfortable dismissing a prokaryote geneticist who criticised Ball's credulousness re: ENCODE because, according to Ball, that geneticist could not appreciate the richness of eukaryotic gene regulation. ENCODE's sweeping statements have been rightly criticised by most biologists qualified to comment. Why does Ball's decade-old poorly argued grudge appear in this book?
Ball entertains heterodoxies, another trait of trespassers, and attacks major, outdated voices, yet another such trait. He argues against a Jacob statement from 1970, but liberally quotes Jacob elsewhere. He argues extensively against Dawkins, someone whom the field has moved far past, yet neglects to discuss Dawkins' quite apt rowing crew metaphor of genes working together, in a book he claims is motivated by his hunger for apt metaphors. Why does Bell forcefully dismiss a wrong hypothesis as a "failed paradigm" (the gene regulatory blobs in Fig 5.2) since he obviously knows of similarly large heterogeneous complexes like the spliceosome and other transcriptional machinery? In his continued focus on the multiplicity of gene functions, he appears to argue that the practice of naming genes after their functions at discovery somehow limits how these genes are viewed when other roles are discovered.
He spends a dismaying amount of time including IQ and IQ genetics. Why the f*ck would he include something so loaded? He states that IQ has a 50% genetic heritability, ridiculously high, without discussing the ways in which heredity measures are loaded. He seems to have read Adam Rutherford, which he understood in only a limited way, but never engages with e.g., Lewontin re: what heredity means. He never discusses the many ways IQ scores are affected by environment and can be meaningfully increased. We must wonder why. Because they put the lie to the high genetic heritability argument? IQ is a magnet for trespassers with a fascination for heterodoxy, which we know by now fully describes Ball. This suggests disturbing things about Ball's and his editors' judgement especially since he claims to want to improve the quality of the popularisation of biology.
There are good things in this book, but there is much else where I don't know who he is actually arguing with. YES popularisation is simplified, overly so, again and again. YES biology is particularly difficult because life is messy. Physics and astrophysics are inherently easier to popularise. This Is Not News.
There is not much of a serious attempt to create new metaphors. "Causal spread" is ... yawn. And the whole "bringing meaning and purpose back to biology" thing, where he wants to give teleology-phobic biology a good lesson, trumpeted so loudly in the prologue and throughout: it gets a whole chapter, but signifies nothing. Is it based on thermodynamics? Emergent properties? Was it largely incoherent and edited down to a nub? Hard to know.
A metaphor which is not ideal but which captures part of of my criticism of Ball's attempts here involves a sailboat. Imagine a blueprint not just for a sailboat but for all the tools you need to build the sailboat, starting with a minimal set left by the last sailboat builder, all designed to be built while on the ocean. The tools and building procedures are designed to function in that environment, using energy and materials from that environment. As the sailboat begins to sail, its design takes advantage of the energy and materials in the ocean to sail distances and repair itself along the way. Large storms can occur, and the sailboat has some ability to recover from storm damage, often with visible damage but still sailing. While sailing, using other tools and procedures described in the blueprint, the sailboat leaves behind little bubbles, each filled with a copy of the blueprints and a minimal set of tools, everything necessary to build another sailboat. Eventually the sailboat succumbs to damage, to impurities incorporated into it from its ocean environment, to leaving behind so many bubbles that it outstrips its ability to sustain itself, or to a design that doesn't reach that far ahead in its lifetime or that broadly into its damaged state.
In this metaphor, it is true that the blueprint of the sailboat is not "the sailboat," but it's a silly statement given the reality of the sailboat's existence within and upon the ocean. That's the genome, and organisms, on planet Earth.
Another approach might be for someone to write a book ostensibly about a single gene that demonstrates the weaknesses of the single-gene perspective. From its first hints to biologists to its structure, its evolutionary history, to eventually learning where and how its expression appears in bodies, the additional roles it seems to have, all the while pointing out things we don't yet know.
One error Ball spends a lot of time criticising in biology -- or rather in popular representations of biology -- is "a gene for", and I agree this is wrong. But saying that the genome is not responsible is a faulty blueprint metaphor; I offer an alternate metaphor at the end of this review. The genome is what is responsible, what would be the alternative? The genome is the system containing A+B+C which interact in complex ways to create a phenotype X+Y+Z that has traits influenced by all genes. Any evolved life is going to have this characteristic. Successful evolution demands it. Fragility will not work. One of the easiest things to get a genome to do is modify its ability to evolve along "expected" environmental axes. The bird's-beak example he uses is exactly one of these. Evolving a beak would never work if pieces of the beak easily evolve out of sync with others.
At the same time, Ball's approach is rather maddening in the ways a non-biologist often expresses when approaching the noisy richness of biology. I should feel comfortable dismissing Ball as a trespassing physicist because Ball felt comfortable dismissing a prokaryote geneticist who criticised Ball's credulousness re: ENCODE because, according to Ball, that geneticist could not appreciate the richness of eukaryotic gene regulation. ENCODE's sweeping statements have been rightly criticised by most biologists qualified to comment. Why does Ball's decade-old poorly argued grudge appear in this book?
Ball entertains heterodoxies, another trait of trespassers, and attacks major, outdated voices, yet another such trait. He argues against a Jacob statement from 1970, but liberally quotes Jacob elsewhere. He argues extensively against Dawkins, someone whom the field has moved far past, yet neglects to discuss Dawkins' quite apt rowing crew metaphor of genes working together, in a book he claims is motivated by his hunger for apt metaphors. Why does Bell forcefully dismiss a wrong hypothesis as a "failed paradigm" (the gene regulatory blobs in Fig 5.2) since he obviously knows of similarly large heterogeneous complexes like the spliceosome and other transcriptional machinery? In his continued focus on the multiplicity of gene functions, he appears to argue that the practice of naming genes after their functions at discovery somehow limits how these genes are viewed when other roles are discovered.
He spends a dismaying amount of time including IQ and IQ genetics. Why the f*ck would he include something so loaded? He states that IQ has a 50% genetic heritability, ridiculously high, without discussing the ways in which heredity measures are loaded. He seems to have read Adam Rutherford, which he understood in only a limited way, but never engages with e.g., Lewontin re: what heredity means. He never discusses the many ways IQ scores are affected by environment and can be meaningfully increased. We must wonder why. Because they put the lie to the high genetic heritability argument? IQ is a magnet for trespassers with a fascination for heterodoxy, which we know by now fully describes Ball. This suggests disturbing things about Ball's and his editors' judgement especially since he claims to want to improve the quality of the popularisation of biology.
There are good things in this book, but there is much else where I don't know who he is actually arguing with. YES popularisation is simplified, overly so, again and again. YES biology is particularly difficult because life is messy. Physics and astrophysics are inherently easier to popularise. This Is Not News.
There is not much of a serious attempt to create new metaphors. "Causal spread" is ... yawn. And the whole "bringing meaning and purpose back to biology" thing, where he wants to give teleology-phobic biology a good lesson, trumpeted so loudly in the prologue and throughout: it gets a whole chapter, but signifies nothing. Is it based on thermodynamics? Emergent properties? Was it largely incoherent and edited down to a nub? Hard to know.
A metaphor which is not ideal but which captures part of of my criticism of Ball's attempts here involves a sailboat. Imagine a blueprint not just for a sailboat but for all the tools you need to build the sailboat, starting with a minimal set left by the last sailboat builder, all designed to be built while on the ocean. The tools and building procedures are designed to function in that environment, using energy and materials from that environment. As the sailboat begins to sail, its design takes advantage of the energy and materials in the ocean to sail distances and repair itself along the way. Large storms can occur, and the sailboat has some ability to recover from storm damage, often with visible damage but still sailing. While sailing, using other tools and procedures described in the blueprint, the sailboat leaves behind little bubbles, each filled with a copy of the blueprints and a minimal set of tools, everything necessary to build another sailboat. Eventually the sailboat succumbs to damage, to impurities incorporated into it from its ocean environment, to leaving behind so many bubbles that it outstrips its ability to sustain itself, or to a design that doesn't reach that far ahead in its lifetime or that broadly into its damaged state.
In this metaphor, it is true that the blueprint of the sailboat is not "the sailboat," but it's a silly statement given the reality of the sailboat's existence within and upon the ocean. That's the genome, and organisms, on planet Earth.
Another approach might be for someone to write a book ostensibly about a single gene that demonstrates the weaknesses of the single-gene perspective. From its first hints to biologists to its structure, its evolutionary history, to eventually learning where and how its expression appears in bodies, the additional roles it seems to have, all the while pointing out things we don't yet know.
October 5, 2024
A 2.5 because though I applaud the intent (show the complexities of how life really works, how many bewilderingly complex layers of control and regulation there are, and how much biology we don't really know, etc.), I thought the execution was not great, his aim at the audience was muddled, and overall he focused on things that were less exciting than I'd hoped.
Mostly, I thought that the use of "new biology" in the title meant the book would focus on some new findings, maybe teach me some stuff that I didn't learn when I went through undergrad/grad in the late 90s and early 00s. But in the end, he spent much more time talking about the discovery of things from the 50s/60s/70s and before than he did about new findings. It just felt like he was constantly using the book as an excuse to talk about his favorite scientists he'd met over the years or rehash his favorite controversies...rather than talk about what we know of the science TODAY. I guess that's it: I was expecting a book on cutting-edge science, and instead it felt like it was much more a cross between history of science and philosophy of science, neither of which really landed well with me. The former felt very much scientific mean girls fighting (yes, sir, I get it, no one likes Dawkins and he was proven wrong on many points, I GET IT, you can stop bringing it up) or scientific fangirling (he really wanted to raise the profile of specific people, and you could tell), and the latter.... I don't know, maybe I'm just not enough of a theorist, but when you start going on about "but what do we mean by 'cause' something?" I start rolling my eyes, because most of the time we've wandered into the realm of philosophy where we're not talking about physical things anymore, and/or it feels like you're using fancy words to describe concepts that are not that fancy.
So, in the end, I wasn't sure who the book was aimed at. Mostly it seemed like people maybe who hadn't taken a science class for 30-50 years. I feel like anyone who learned their in-depth science before 2000 is not going to learn very much from this book. Also though he talks about wanting to fight back against science communication being too simplistic, I don't think the average reader could follow this easily.
And I admit, I was also puzzled/surprised a bit by his choice of topics. For instance, I'm a cell biologist, so I was looking forward to the chapters on cells and tissues. Tell me neat things about cell function! Or about tissue specialization! But no! Those chapters were mostly embryology and developmental biology: how cells differentiate and how different tissues are formed in the embryo. And I will confess, developmental biology is one of my least favorite biologies - when I was taught it, it was very descriptive (why do these things happen? We don't know. Here, let's have you memorize what each of these cells becomes....), and though the author does put in some new findings since I was in college in the late 90s, the upshot is that we STILL don't know how it works. So thus...let's take a lot of time describing what each of these cells becomes and then say a few sentences about the actual current research into what controls that! It just wasn't the ratio of new to old information I was hoping for.
Mostly, I thought that the use of "new biology" in the title meant the book would focus on some new findings, maybe teach me some stuff that I didn't learn when I went through undergrad/grad in the late 90s and early 00s. But in the end, he spent much more time talking about the discovery of things from the 50s/60s/70s and before than he did about new findings. It just felt like he was constantly using the book as an excuse to talk about his favorite scientists he'd met over the years or rehash his favorite controversies...rather than talk about what we know of the science TODAY. I guess that's it: I was expecting a book on cutting-edge science, and instead it felt like it was much more a cross between history of science and philosophy of science, neither of which really landed well with me. The former felt very much scientific mean girls fighting (yes, sir, I get it, no one likes Dawkins and he was proven wrong on many points, I GET IT, you can stop bringing it up) or scientific fangirling (he really wanted to raise the profile of specific people, and you could tell), and the latter.... I don't know, maybe I'm just not enough of a theorist, but when you start going on about "but what do we mean by 'cause' something?" I start rolling my eyes, because most of the time we've wandered into the realm of philosophy where we're not talking about physical things anymore, and/or it feels like you're using fancy words to describe concepts that are not that fancy.
So, in the end, I wasn't sure who the book was aimed at. Mostly it seemed like people maybe who hadn't taken a science class for 30-50 years. I feel like anyone who learned their in-depth science before 2000 is not going to learn very much from this book. Also though he talks about wanting to fight back against science communication being too simplistic, I don't think the average reader could follow this easily.
And I admit, I was also puzzled/surprised a bit by his choice of topics. For instance, I'm a cell biologist, so I was looking forward to the chapters on cells and tissues. Tell me neat things about cell function! Or about tissue specialization! But no! Those chapters were mostly embryology and developmental biology: how cells differentiate and how different tissues are formed in the embryo. And I will confess, developmental biology is one of my least favorite biologies - when I was taught it, it was very descriptive (why do these things happen? We don't know. Here, let's have you memorize what each of these cells becomes....), and though the author does put in some new findings since I was in college in the late 90s, the upshot is that we STILL don't know how it works. So thus...let's take a lot of time describing what each of these cells becomes and then say a few sentences about the actual current research into what controls that! It just wasn't the ratio of new to old information I was hoping for.
May 3, 2024
The author spends the first 50 pages telling you that everything you know is wrong and you don't know nothing. He continues this tone throughout the book and it's really annoying. The level of this book is graduate school. Disappointing for someone that just wants to learn about the state of modern biology.
May 9, 2024
"Put simply, framing the issue of what makes us the way we are as “nature vs. nurture,” and especially “genes vs. environment,” deforms the causal landscape of living systems into a shape it does not fit, and so we can no longer make out what it truly looks like. As with many recalcitrant questions, the way to resolve the “nature vs. nurture” argument is not to answer it but to recognize that it is the wrong question."
This is an odd duck of a book: the third recent book on biology to take on a gene-centric view of biology, along with Siddhartha Mukherjee's Song of the Cell and Aria Alfonso Martinez' The Master Builder. As the title attests, Ball's How Life Works is the most ambitious of the three. Ball, former editor of Nature and committed to communicating complexity, determined to show as much of the complex, messy, impossible-to-untangle science of how bodies work, from the molecular to the organism level. His goal is both to frustrate attempts to oversimplify things, especially the idea of DNA as a blueprint, and to show the various ways that physical and chemical laws play out through biology to create people, inheritance, diversity and change. And that those things are not always the same things.
The book is awash with frustrations. Ball decries the dangers of metaphors but deploys some very simplistic ones in criticising points of view that frustrate him. He frequently name checks issues with concepts he supports, like emergence, or attributing agency to physical processes. I suspect he is occasionally guilty of describing complexity simply to show his audience that this stuff is harder than they suspect to really understand or predict. It is not always convincing, either, in convincing on some of Ball's deeply held beliefs around the ways that life embodies purpose. There are a few too many Dennett quotes.
But I can't help but admire the book's ambition, intent, and yes even execution. I have read literally dozens of books about DNA, but never have I had such a detailed explanation of the actual process of replication, epigenetic activations and the sheer bloody chaos of it all. You can almost visualise the process - much less linear, much more vibrant, than most flattened descriptions make it seem. This serves one of his central arguments - that evolution prioritised developing sophisticated and efficient biological processes over just replicating genes. That our cells can activate and deploy genes in variously innovative and varied ways throughout our bodies might matter just as much as which genes are available for deployment. If a group of genes can all do roughly the same thing, it might be simply which is most efficient to reach that makes a difference. Most of our genes do not code for protein but rather are used in replication processes (we think so much is still unclear), including many strongly identified with rare diseases. In other words, it is all far more intricate than we should expect to be able to simply understand because we've decoded a genome into letters.
This is not to say that Ball decries inheritance. But he does point out that what has been successful in identifying inheritance is the statistic-crunching Genome-Wide Association Studies, which track the correlation between physical disease and genes, not any numerically significant number of attempts to understand *how* genes work. This process is successful in identifying risk but not so much in identifying treatments.
It is all a lot to think about, and if, like its subject matter, this book is messy and occasionally infuriating and often feels slightly too much, it is better by far than the streamlined certainty too ,much of our current science presents.
This is an odd duck of a book: the third recent book on biology to take on a gene-centric view of biology, along with Siddhartha Mukherjee's Song of the Cell and Aria Alfonso Martinez' The Master Builder. As the title attests, Ball's How Life Works is the most ambitious of the three. Ball, former editor of Nature and committed to communicating complexity, determined to show as much of the complex, messy, impossible-to-untangle science of how bodies work, from the molecular to the organism level. His goal is both to frustrate attempts to oversimplify things, especially the idea of DNA as a blueprint, and to show the various ways that physical and chemical laws play out through biology to create people, inheritance, diversity and change. And that those things are not always the same things.
The book is awash with frustrations. Ball decries the dangers of metaphors but deploys some very simplistic ones in criticising points of view that frustrate him. He frequently name checks issues with concepts he supports, like emergence, or attributing agency to physical processes. I suspect he is occasionally guilty of describing complexity simply to show his audience that this stuff is harder than they suspect to really understand or predict. It is not always convincing, either, in convincing on some of Ball's deeply held beliefs around the ways that life embodies purpose. There are a few too many Dennett quotes.
But I can't help but admire the book's ambition, intent, and yes even execution. I have read literally dozens of books about DNA, but never have I had such a detailed explanation of the actual process of replication, epigenetic activations and the sheer bloody chaos of it all. You can almost visualise the process - much less linear, much more vibrant, than most flattened descriptions make it seem. This serves one of his central arguments - that evolution prioritised developing sophisticated and efficient biological processes over just replicating genes. That our cells can activate and deploy genes in variously innovative and varied ways throughout our bodies might matter just as much as which genes are available for deployment. If a group of genes can all do roughly the same thing, it might be simply which is most efficient to reach that makes a difference. Most of our genes do not code for protein but rather are used in replication processes (we think so much is still unclear), including many strongly identified with rare diseases. In other words, it is all far more intricate than we should expect to be able to simply understand because we've decoded a genome into letters.
This is not to say that Ball decries inheritance. But he does point out that what has been successful in identifying inheritance is the statistic-crunching Genome-Wide Association Studies, which track the correlation between physical disease and genes, not any numerically significant number of attempts to understand *how* genes work. This process is successful in identifying risk but not so much in identifying treatments.
It is all a lot to think about, and if, like its subject matter, this book is messy and occasionally infuriating and often feels slightly too much, it is better by far than the streamlined certainty too ,much of our current science presents.
July 14, 2025
In modern Western society, almost everyone learns to read and write. Unfortunately, not everyone who can write, should write. Philip Ball exemplifies this point in his book.
The author's main argument is that life is complex, and the gene-centric view of biology is shortsighted and limits our understanding. If he had stuck to this premise, it might have been a half-decent book. However, he repeatedly ridicules those who believe that genes play any causal role in how life unfolds. He resorts to poor analogies, such as on page 52, where he suggests:
genes + magic → proteins + magic → cells + magic = tissues and bodies
Beyond that, he is clearly on the attack and frequently inserts passive-aggressive remarks, such as on page 55:
"The instructions for how the egg develops are written in the linear sequence of bases along the DNA of the germ cells." (Spoiler: they are not.)
His preferred explanation is that of causal emergence. He argues that the complexity of organisms cannot be reduced to the level of genes and therefore must arise from a higher order of organization. However, when we examine the definition of causal emergence (Mediano et al., 2022; https://doi.org/10.1098/rsta.2021.0246), we can see where this reasoning falters:
“Causal emergence is, therefore, defined as the capability of some supervenient feature to provide predictive power that cannot be reduced to underlying microscale phenomena—up to order k.”
Roughly translated, this means that higher-order phenomena (such as gene networks) may have predictive power that cannot be fully reduced to the gene level. A bit further in the same paper, the authors explain:
“In summary, these equations imply that causal emergence takes place when groups of variables influence the future of the system together, but not separately.”
Applied to genomics, this would imply that in a causally emergent system, knockdowns or knockouts of individual genes would not affect the system's state. While it's true that not every gene perturbation yields a visible phenotype, there are countless examples where such manipulations have clear, often profound effects. Thus, the book’s central argument does not hold.
It seems the author acknowledges the complexity involved in going from protein-coding genes to a fully developed organism. However, he presents this as a novel revelation, which is unfair to the decades of rigorous work already done in this field. The centrality of gene regulation in development has been well-known and widely accepted for a long time. Ball acts as though this is groundbreaking insight while neglecting the fact that gene regulation is fundamentally genomic: regulatory regions are part of the genome, regulatory RNAs are encoded in the genome, and transcription factors are products of the genome. Yes, the process is complex—but it remains genomic.
As I don't want to write an entire book in response, I’ll refrain from detailing every preposterous claim, such as the suggestion that having two legs is not genetic but merely one possible developmental outcome.
For those genuinely interested in the fascinating complexity of organismal development, I recommend Endless Forms Most Beautiful by Sean Carroll. That book invites you to marvel at how life works—without a hidden agenda.
The author's main argument is that life is complex, and the gene-centric view of biology is shortsighted and limits our understanding. If he had stuck to this premise, it might have been a half-decent book. However, he repeatedly ridicules those who believe that genes play any causal role in how life unfolds. He resorts to poor analogies, such as on page 52, where he suggests:
genes + magic → proteins + magic → cells + magic = tissues and bodies
Beyond that, he is clearly on the attack and frequently inserts passive-aggressive remarks, such as on page 55:
"The instructions for how the egg develops are written in the linear sequence of bases along the DNA of the germ cells." (Spoiler: they are not.)
His preferred explanation is that of causal emergence. He argues that the complexity of organisms cannot be reduced to the level of genes and therefore must arise from a higher order of organization. However, when we examine the definition of causal emergence (Mediano et al., 2022; https://doi.org/10.1098/rsta.2021.0246), we can see where this reasoning falters:
“Causal emergence is, therefore, defined as the capability of some supervenient feature to provide predictive power that cannot be reduced to underlying microscale phenomena—up to order k.”
Roughly translated, this means that higher-order phenomena (such as gene networks) may have predictive power that cannot be fully reduced to the gene level. A bit further in the same paper, the authors explain:
“In summary, these equations imply that causal emergence takes place when groups of variables influence the future of the system together, but not separately.”
Applied to genomics, this would imply that in a causally emergent system, knockdowns or knockouts of individual genes would not affect the system's state. While it's true that not every gene perturbation yields a visible phenotype, there are countless examples where such manipulations have clear, often profound effects. Thus, the book’s central argument does not hold.
It seems the author acknowledges the complexity involved in going from protein-coding genes to a fully developed organism. However, he presents this as a novel revelation, which is unfair to the decades of rigorous work already done in this field. The centrality of gene regulation in development has been well-known and widely accepted for a long time. Ball acts as though this is groundbreaking insight while neglecting the fact that gene regulation is fundamentally genomic: regulatory regions are part of the genome, regulatory RNAs are encoded in the genome, and transcription factors are products of the genome. Yes, the process is complex—but it remains genomic.
As I don't want to write an entire book in response, I’ll refrain from detailing every preposterous claim, such as the suggestion that having two legs is not genetic but merely one possible developmental outcome.
For those genuinely interested in the fascinating complexity of organismal development, I recommend Endless Forms Most Beautiful by Sean Carroll. That book invites you to marvel at how life works—without a hidden agenda.
February 5, 2025
This was some solid science writing, but not at all that revolutionary as advertised; good thing the author draws our attention to the shortcoming of the central dogma of molecular biology (DNA makes RNA and RNA makes protein), coined by Francis Crick (in 1957); yes you need a molecular apparatus, cellular structures (ribosomes, Golgi apparatus, enzymes etc.) to make life happen, and yes epigenetics plays a far more important role than originally envisioned, but this can all be accomodated in available knowledge on the biology of life; so no revolutions, just science at work; ever getting better in explanatory power.
May 24, 2025
I thought this book was excellent, especially the evolutionary-development and the making/hacking chapters. The author argues for the recognition of agency in biology which I remain unconvinced of. He also argues against the genome as a blueprint which I feel is a bit of a straw man (surely most biologists see it more of a recipe which depends on environmental factors). However, overall, the book describes some of the recent findings at the cutting edge of biology with aplomb, and provides much food for thought, which I very much appreciated.
April 23, 2024
Nature dergisindeki yorumu tercüme ettim… Verimli bir bilim yazarından iddialı bir kitap
İnsan Genomu Projesi'nin 20 yıl önce tamamlanması ve bu yıl 70. yaşını kutlayan çift sarmalın keşfedilmesiyle aslında hayatın nasıl işlediğinin bilindiği artık düşünülebilinir. Fizikte “Büyük Birleştirici Teori” olarak adlandırılan arayış, nesiller boyunca en hırslı zihinleri meşgul etmiştir, ama ne yazık ki sonuçsuz kalmıştır. Ancak yaşam bilimlerinde yaklaşık 100 yıllık bir sürede dört “büyük birleştirici teori” bulunması başarılmıştır. Bunlardan üçü iyi bilinmektedir: i) Hücre teorisi yani tüm yaşam, yalnızca mevcut hücrelerden meydana gelen yeni hücrelerden oluşmaktadır; ii) Darwin'in doğal seçilim yoluyla evrim teorisi; ve iii) evrensel genetik teorisi yani tüm yaşam, DNA molekülüne yazılan şifre tarafından kodlanmaktadır. Daha az önemli olmayan dördüncüsü, kemiosmoz adını almakta ve bu teori tüm canlıların çevrelerinden yakıt alarak ve bunu sürekli bir kimyasal reaksiyonda kullanarak nasıl yaşadıklarını anlatmaktadır. Özetle, yaşam daha önceki yapıya göre değişiklik geçirerek meydana gelen ve enerjisini çevreden alan hücrelerden oluşur. Yazar fizikçi çünkü ! :)
Bununla birlikte, biyoloji fazlasıyla karmaşıktır ve her ne kadar dünya üzerindeki tüm yaşamı tanımlayacak bu yasalara sahip olsak da, kimyanın biyolojiye nasıl dönüştüğüne dair anlayışımız ve bilgilerimiz henüz tamamlanmış olmaktan çok çok uzaktır. Bu büyük birleştirici teoriler inkar edilemez ancak karmaşıktır ve ayrıntılardan yoksundur ve biyolojide anlaşılması zor olan bu karmaşıklar asıl olarak moleküler düzeyinde yatmaktadır. Aslen fizikçi olan Philip Ball'un mükemmel yeni kitabında işaret ettiği gibi, bu durum, görünmez bir virüsün 2020'de dünyayı altüst ettiği, milyonları öldürdüğü ve çok daha fazlasına bulaştığı zamana kadar hiçbir yerde bu kadar açık bir şekilde ortaya çıkmamıştır. Virüs bazı insanlar için öldürücü veya aylarca, hatta yıllarca sürecek sayısız semptomlara neden olurken, diğerleri için hafif bir soğuk algınlığına benzemekte, ve hatta tamamen semptomsuz olmaktadır. Bunun neden böyle olduğu hala tam olarak bilinmemektedir.
Yaşam Nasıl İşlemektedir? sorusu oldukça fazla kullanılan “ yaşam nedir?" sorusundan çok daha ilginç ve doğru bir sorudur.
Daha çok içinde taahhütsüz bir kuantum kedisi olan varsayımsal kutusuyla ünlü Erwin Schrödinger'in 1944'te bir dizi etkili konferansında verdiği ve beraberindeki kitabında sorduğu soru “ yaşam nedir?” idi ve o zamandan beri bu soru, derin görünmek isteyen birçok kişi tarafından kullanılmaktadır. Bu soru büyük ölçüde anlamsız ve bir bakıma bilimsel düşüncenin kendisine aykırı durmaktadır. Bir şeyin ne olduğuyla daha az ilgilenilmeli ve daha çok ne yaptığına odaklanılmalıdır. Bir canlıyı tanımlamak aslında bir tür yaratılışçı sorudur, çünkü değişmez bir ideal tip olduğunu ima etmektedir, ancak bu büyük birleştirici teorilerden birine yani canlıların dört boyutlu olduğu, zaman ve uzay içinde sürekli değiştiği yönündeki Darwinci ilkeye ters düşmektedir.
Ancak yaşam, kültürlerin derinliklerine kadar kök salmış bir fikirdir: yaşamsal bir güç, yaşam kıvılcımı, diri ile ölüyü ayıran anlaşılması zor ama temel bir niteliktir. Yaşam nedir? Kesin olarak tespit etmek zordur, ancak 1964'teki ABD Yargıcı Potter Stewart'ın söylediği gibi bunu gördüğümüzde zaman biliriz ve anlarız (kuşkusuz, aslında pornografinin soyut tanımına atıfta bulunuyordu).
Ball, yaşamın kötü karmaşıklıklarını açıklamak ve keşfetmek için metaforlara ve analojilere güvenildiğini ancak hiçbirinin yeterli olmadığını belirtmektedir. Bizlere hücrelerin makine olduğu öğretilmektedir, ancak icat edilen hiçbir makine en basit hücre gibi davranmaz; DNA'nın bir kod ya da bir plan olduğu söylenmektedir ama aslında ikisi de değildir; Beynin bir bilgisayar olduğu bilgisi verilmektedir, ancak hiçbir bilgisayar beyin gibi davranmaz.
Bilinen evrendeki en karmaşık varlıkları, yani yaşayan varlıkları basit bir açıklamaya indirgemeye çalışmak gerçekten çok komik olmaktadır. Karmaşık sistemleri çözmede anlatılar yaparak tatmin olmayı çalışılmaktadır, ancak evrimin insanlıktan 4 milyar yıllık bir üstünlüğü vardır ama onun hiçbir planı yoktur, ayrıca zeki meyvelerinden biri olan insan tarafından anlaşılma konusunda da bir derdi yoktur. 1953'te DNA'nın çift sarmal yapısını yayınlayan ikiliden biri olan James Watson, bir keresinde ikilinin diğeri olan Francis Crick'in Cambridge'deki Eagle pub'a daldığını ve “yaşamın sırrını" keşfettiklerini ilan ettiğini yazmıştır. (gerçi 2017'de Watson, tüm sahneyi dramatik bir etki yaratmak için icat ettiğini itiraf ettir). Ball, bunu sanatla ya da aşırı güzellikteki diğer konularda yapmaya çalışmadığına dikkat çekmektedir: hiçbir okuyucu ya da bilim adamı "Dickens'ın sırrını" izole etmeye ve damıtmaya çalışmıyor der.
Bu basitleştirmeler ve analojiler ortaya atılmaktadır çünkü hem "işler bundan biraz daha karmaşık" şeklindeki küçümseyici söylemi basitçe ortaya atmak hem de öğrencilerin bunalmalarını ve sıkılmalarını görmek hiç de iyi değildir. Ancak Ball, eğitimde kullanılan modellerin daha iyi anlaşılması için karmaşıklar azaltılırken, aslında karmaşıklığın varlığının da yok edilip edilmediğini merak etmektedir; sanki bir daha asla biyoloji hakkında düşünmek zorunda kalmamak için bu karmaşıklık aradan çıkarılmaya çalışılıyormuş gibi gelmektedir. Burada istatistikçi George Box'ın daha güzel bir söylemi akla gelmektedir: Tüm modeller yanlıştır, ancak bazıları yine de faydalıdır.
Ball, genetikte sıklıkla yapıldığı gibi, dili kullanarak güzel bir benzetme yapmaktadır. Sözlükteki kelimelerden kitaplara ve edebiyata nasıl geçilir diye sorar? Şöyle bir formül söylemektedir: kelimeler (+sihir) > cümleler (+sihir) > bölümler ve kitaplar. Canlı bir organizmada bunun karşılığı ise şudur: genler (+sihir) > proteinler (+sihir) > hücreler (+sihir) > dokular ve vücutlar.
Tabii ki burada sihir doğaüstü demek değil, bu sadece henüz bilinmeyen veya basit bir şekilde açıklanamayan, yaşamın işleyişinin özü olan şeydir.
Kitap şu akış şemasını takip etmektedir: Genetiğin temelleri hakkında bir genel bilgilendirme vardır ama insanların bunu öğretme ve genler hakkında düşünme şekli genetikçilerin bildikleri şekilde değildir. İnsanın karmaşık özellikleri veya davranışları için belirli genler yoktur, ancak genellikle "Bilim adamları şunun için bu geni keşfediyor" şeklinde manşetlerde dile getirilen yanlış kanı kültürel olarak yerleşmiştir. Ortaya çıkan kanıtlar, bilimin günümüzde çocuklarda genetiği öğretme şeklinin yalnızca bu hatayı değil, aynı zamanda uzun bir süredir terk edilmiş olan ırkçı varoluşçuluğun bir versiyonunu da bilim tarafından güçlendirdiğini göstermektedir.
Ball, genlerden proteinlere, hücrelere ve ağlara doğru ilerlemekte ve bunu yaparak kimyadan biyolojiye götüren keşfedilmemiş büyünün/sihrin içinde saplanıp kalınmasını, bu arada doğa mı çevre mi gibi işin içinden çıkılmaz bir fikrin de göz ardı edilmesini sağlamaktadır: “ yaşam yalnızca çevresiyle ilişkili olarak işler diye ne kadar vurgulasam azdır" diye belirtmektedir.
Ball müthiş bir yazar; inanılmaz derecede çeşitli konulardaki kitapları kıskanılacak ve yetersiz hissettirecek oranda karşımızda durmaktadır. Burada çok sayıda iyi araştırılmış bilgi vardır, hatta sıradan okuyucu için hazmetilmesi biraz zor bazı ayrıntılar da vardır ve açığa çıkarılmayacak kadar karmaşık ve dolayısıyla aydınlatıcı olmayan proteinlerin siyah-beyaz çizimlerinin faydasını sorgulanabilir. Ancak bunun dışında kitap, yaşamı anlamaya yönelik bitmek bilmeyen arayışlar için önemli bir başlangıç noktası görevi görmektedir. Sonuçta “ Yaşam nedir?” yararlı bir cevabı olmayan bir sorudur. “ Yaşam nasıl işliyor?" İşte gelecek vaat eden biyolog nesillerini beşikten mezara yönlendirmesi gereken soru budur.
İnsan Genomu Projesi'nin 20 yıl önce tamamlanması ve bu yıl 70. yaşını kutlayan çift sarmalın keşfedilmesiyle aslında hayatın nasıl işlediğinin bilindiği artık düşünülebilinir. Fizikte “Büyük Birleştirici Teori” olarak adlandırılan arayış, nesiller boyunca en hırslı zihinleri meşgul etmiştir, ama ne yazık ki sonuçsuz kalmıştır. Ancak yaşam bilimlerinde yaklaşık 100 yıllık bir sürede dört “büyük birleştirici teori” bulunması başarılmıştır. Bunlardan üçü iyi bilinmektedir: i) Hücre teorisi yani tüm yaşam, yalnızca mevcut hücrelerden meydana gelen yeni hücrelerden oluşmaktadır; ii) Darwin'in doğal seçilim yoluyla evrim teorisi; ve iii) evrensel genetik teorisi yani tüm yaşam, DNA molekülüne yazılan şifre tarafından kodlanmaktadır. Daha az önemli olmayan dördüncüsü, kemiosmoz adını almakta ve bu teori tüm canlıların çevrelerinden yakıt alarak ve bunu sürekli bir kimyasal reaksiyonda kullanarak nasıl yaşadıklarını anlatmaktadır. Özetle, yaşam daha önceki yapıya göre değişiklik geçirerek meydana gelen ve enerjisini çevreden alan hücrelerden oluşur. Yazar fizikçi çünkü ! :)
Bununla birlikte, biyoloji fazlasıyla karmaşıktır ve her ne kadar dünya üzerindeki tüm yaşamı tanımlayacak bu yasalara sahip olsak da, kimyanın biyolojiye nasıl dönüştüğüne dair anlayışımız ve bilgilerimiz henüz tamamlanmış olmaktan çok çok uzaktır. Bu büyük birleştirici teoriler inkar edilemez ancak karmaşıktır ve ayrıntılardan yoksundur ve biyolojide anlaşılması zor olan bu karmaşıklar asıl olarak moleküler düzeyinde yatmaktadır. Aslen fizikçi olan Philip Ball'un mükemmel yeni kitabında işaret ettiği gibi, bu durum, görünmez bir virüsün 2020'de dünyayı altüst ettiği, milyonları öldürdüğü ve çok daha fazlasına bulaştığı zamana kadar hiçbir yerde bu kadar açık bir şekilde ortaya çıkmamıştır. Virüs bazı insanlar için öldürücü veya aylarca, hatta yıllarca sürecek sayısız semptomlara neden olurken, diğerleri için hafif bir soğuk algınlığına benzemekte, ve hatta tamamen semptomsuz olmaktadır. Bunun neden böyle olduğu hala tam olarak bilinmemektedir.
Yaşam Nasıl İşlemektedir? sorusu oldukça fazla kullanılan “ yaşam nedir?" sorusundan çok daha ilginç ve doğru bir sorudur.
Daha çok içinde taahhütsüz bir kuantum kedisi olan varsayımsal kutusuyla ünlü Erwin Schrödinger'in 1944'te bir dizi etkili konferansında verdiği ve beraberindeki kitabında sorduğu soru “ yaşam nedir?” idi ve o zamandan beri bu soru, derin görünmek isteyen birçok kişi tarafından kullanılmaktadır. Bu soru büyük ölçüde anlamsız ve bir bakıma bilimsel düşüncenin kendisine aykırı durmaktadır. Bir şeyin ne olduğuyla daha az ilgilenilmeli ve daha çok ne yaptığına odaklanılmalıdır. Bir canlıyı tanımlamak aslında bir tür yaratılışçı sorudur, çünkü değişmez bir ideal tip olduğunu ima etmektedir, ancak bu büyük birleştirici teorilerden birine yani canlıların dört boyutlu olduğu, zaman ve uzay içinde sürekli değiştiği yönündeki Darwinci ilkeye ters düşmektedir.
Ancak yaşam, kültürlerin derinliklerine kadar kök salmış bir fikirdir: yaşamsal bir güç, yaşam kıvılcımı, diri ile ölüyü ayıran anlaşılması zor ama temel bir niteliktir. Yaşam nedir? Kesin olarak tespit etmek zordur, ancak 1964'teki ABD Yargıcı Potter Stewart'ın söylediği gibi bunu gördüğümüzde zaman biliriz ve anlarız (kuşkusuz, aslında pornografinin soyut tanımına atıfta bulunuyordu).
Ball, yaşamın kötü karmaşıklıklarını açıklamak ve keşfetmek için metaforlara ve analojilere güvenildiğini ancak hiçbirinin yeterli olmadığını belirtmektedir. Bizlere hücrelerin makine olduğu öğretilmektedir, ancak icat edilen hiçbir makine en basit hücre gibi davranmaz; DNA'nın bir kod ya da bir plan olduğu söylenmektedir ama aslında ikisi de değildir; Beynin bir bilgisayar olduğu bilgisi verilmektedir, ancak hiçbir bilgisayar beyin gibi davranmaz.
Bilinen evrendeki en karmaşık varlıkları, yani yaşayan varlıkları basit bir açıklamaya indirgemeye çalışmak gerçekten çok komik olmaktadır. Karmaşık sistemleri çözmede anlatılar yaparak tatmin olmayı çalışılmaktadır, ancak evrimin insanlıktan 4 milyar yıllık bir üstünlüğü vardır ama onun hiçbir planı yoktur, ayrıca zeki meyvelerinden biri olan insan tarafından anlaşılma konusunda da bir derdi yoktur. 1953'te DNA'nın çift sarmal yapısını yayınlayan ikiliden biri olan James Watson, bir keresinde ikilinin diğeri olan Francis Crick'in Cambridge'deki Eagle pub'a daldığını ve “yaşamın sırrını" keşfettiklerini ilan ettiğini yazmıştır. (gerçi 2017'de Watson, tüm sahneyi dramatik bir etki yaratmak için icat ettiğini itiraf ettir). Ball, bunu sanatla ya da aşırı güzellikteki diğer konularda yapmaya çalışmadığına dikkat çekmektedir: hiçbir okuyucu ya da bilim adamı "Dickens'ın sırrını" izole etmeye ve damıtmaya çalışmıyor der.
Bu basitleştirmeler ve analojiler ortaya atılmaktadır çünkü hem "işler bundan biraz daha karmaşık" şeklindeki küçümseyici söylemi basitçe ortaya atmak hem de öğrencilerin bunalmalarını ve sıkılmalarını görmek hiç de iyi değildir. Ancak Ball, eğitimde kullanılan modellerin daha iyi anlaşılması için karmaşıklar azaltılırken, aslında karmaşıklığın varlığının da yok edilip edilmediğini merak etmektedir; sanki bir daha asla biyoloji hakkında düşünmek zorunda kalmamak için bu karmaşıklık aradan çıkarılmaya çalışılıyormuş gibi gelmektedir. Burada istatistikçi George Box'ın daha güzel bir söylemi akla gelmektedir: Tüm modeller yanlıştır, ancak bazıları yine de faydalıdır.
Ball, genetikte sıklıkla yapıldığı gibi, dili kullanarak güzel bir benzetme yapmaktadır. Sözlükteki kelimelerden kitaplara ve edebiyata nasıl geçilir diye sorar? Şöyle bir formül söylemektedir: kelimeler (+sihir) > cümleler (+sihir) > bölümler ve kitaplar. Canlı bir organizmada bunun karşılığı ise şudur: genler (+sihir) > proteinler (+sihir) > hücreler (+sihir) > dokular ve vücutlar.
Tabii ki burada sihir doğaüstü demek değil, bu sadece henüz bilinmeyen veya basit bir şekilde açıklanamayan, yaşamın işleyişinin özü olan şeydir.
Kitap şu akış şemasını takip etmektedir: Genetiğin temelleri hakkında bir genel bilgilendirme vardır ama insanların bunu öğretme ve genler hakkında düşünme şekli genetikçilerin bildikleri şekilde değildir. İnsanın karmaşık özellikleri veya davranışları için belirli genler yoktur, ancak genellikle "Bilim adamları şunun için bu geni keşfediyor" şeklinde manşetlerde dile getirilen yanlış kanı kültürel olarak yerleşmiştir. Ortaya çıkan kanıtlar, bilimin günümüzde çocuklarda genetiği öğretme şeklinin yalnızca bu hatayı değil, aynı zamanda uzun bir süredir terk edilmiş olan ırkçı varoluşçuluğun bir versiyonunu da bilim tarafından güçlendirdiğini göstermektedir.
Ball, genlerden proteinlere, hücrelere ve ağlara doğru ilerlemekte ve bunu yaparak kimyadan biyolojiye götüren keşfedilmemiş büyünün/sihrin içinde saplanıp kalınmasını, bu arada doğa mı çevre mi gibi işin içinden çıkılmaz bir fikrin de göz ardı edilmesini sağlamaktadır: “ yaşam yalnızca çevresiyle ilişkili olarak işler diye ne kadar vurgulasam azdır" diye belirtmektedir.
Ball müthiş bir yazar; inanılmaz derecede çeşitli konulardaki kitapları kıskanılacak ve yetersiz hissettirecek oranda karşımızda durmaktadır. Burada çok sayıda iyi araştırılmış bilgi vardır, hatta sıradan okuyucu için hazmetilmesi biraz zor bazı ayrıntılar da vardır ve açığa çıkarılmayacak kadar karmaşık ve dolayısıyla aydınlatıcı olmayan proteinlerin siyah-beyaz çizimlerinin faydasını sorgulanabilir. Ancak bunun dışında kitap, yaşamı anlamaya yönelik bitmek bilmeyen arayışlar için önemli bir başlangıç noktası görevi görmektedir. Sonuçta “ Yaşam nedir?” yararlı bir cevabı olmayan bir sorudur. “ Yaşam nasıl işliyor?" İşte gelecek vaat eden biyolog nesillerini beşikten mezara yönlendirmesi gereken soru budur.
Read
November 24, 2024the revolutionary vanguard must defend against Dawkinite gene-centrism on all fronts
January 15, 2024
This book is still buzzing in my head. The author talks about metaphors in biology, states that life is a meaning-making system, and emphasizes the importance of broadly understood agency and purposefulness in all studied matter. These are just a few interesting tropes in this solid set of biological concepts. PS, it turns out that DNA is not the magic key to the mystery of life! In many respects we are „not even wrong”.
January 19, 2025
A great book about the science of life, biology... and not just the biology you learned 50 years ago in middle school. This book is about the biology that researchers are studying today. And about their work to explain life and understand how it works and when it doesn't work properly, what to do to fix it. There are many great references in its bibliography and the author has excellent notes. And IMO this will be a fascinating read for even those who know Nothing about the subject.
June 30, 2025
It is the Book that should be shown to everyone... it is the book we are looking for... the description is the answer to my questions related to the emergence and evolution of Life and not only...
Wonderful! It's amazing how we attract the answers to our lofty questions... thank you Infinite! Blessed time! Bless the voice of the Heart, Infinite...💖
Wonderful! It's amazing how we attract the answers to our lofty questions... thank you Infinite! Blessed time! Bless the voice of the Heart, Infinite...💖
March 9, 2025
Superb. Starts by the low layers of life and climbs to the top. Wow.
April 20, 2024
A ideia central é muito importante, mas o livro falha em toda a linha, pelo menos na sua comunicação para com quem não é da área. A ideia é resumida nesta simples frase, expandida no primeiro capítulo, que é aquele que vale mesmo a pena ler:
"Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works—the idea of the genome as a blueprint, of genes as instructions for building an organism, of proteins as precisely tailored molecular machines, of cells as entities with fixed identities, and more—have been exposed as incomplete, misleading, or wrong."
Contudo, discutir toda a nossa biologia sem fazer um esforço mínimo por explicar o que está a discutir é como chover no molhado. A questão não tem que ver com complexidade. A biologia não é mais complexa que a astrofísica, e no entanto todos nós percebemos o que Carl Sagan tem para dizer. O problema aqui é a total inabilidade do autor para construir pontes entre o conhecimento específico da biologia e o da realidade concreta.
Se realmente havia aqui interesse em comunicar esta ideia para um público mais vasto, e considero que devia haver, tendo em conta as enormes implicações do que está aqui a ser descrito, o autor falha em toda a linha. Demonstra uma incapacidade atroz na construção de metáforas que pudessem traduzir o que se passa no domínio da biologia.
O primeiro capítulo é aquele que compensa a leitura, porque através de vários casos simples Ball deita por terra a ideia de que tudo vem inscrito nos genes. Não admira que ao longo da última década tenhamos visto o declínio do enfoque nos mesmos. Contudo, as ideias centrais acabaram passando para os média e contaminaram o imaginário das pessoas. A sociedade acredita piamente nos genes como base daquilo que somos, indo ao ponto de acreditar que somos marcados e inalteráveis por causa dos mesmos. É preciso desconstruir estes mitos, mas tal não vai acontecer com livros como este. Uma oportunidade perdida.
"Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works—the idea of the genome as a blueprint, of genes as instructions for building an organism, of proteins as precisely tailored molecular machines, of cells as entities with fixed identities, and more—have been exposed as incomplete, misleading, or wrong."
Contudo, discutir toda a nossa biologia sem fazer um esforço mínimo por explicar o que está a discutir é como chover no molhado. A questão não tem que ver com complexidade. A biologia não é mais complexa que a astrofísica, e no entanto todos nós percebemos o que Carl Sagan tem para dizer. O problema aqui é a total inabilidade do autor para construir pontes entre o conhecimento específico da biologia e o da realidade concreta.
Se realmente havia aqui interesse em comunicar esta ideia para um público mais vasto, e considero que devia haver, tendo em conta as enormes implicações do que está aqui a ser descrito, o autor falha em toda a linha. Demonstra uma incapacidade atroz na construção de metáforas que pudessem traduzir o que se passa no domínio da biologia.
O primeiro capítulo é aquele que compensa a leitura, porque através de vários casos simples Ball deita por terra a ideia de que tudo vem inscrito nos genes. Não admira que ao longo da última década tenhamos visto o declínio do enfoque nos mesmos. Contudo, as ideias centrais acabaram passando para os média e contaminaram o imaginário das pessoas. A sociedade acredita piamente nos genes como base daquilo que somos, indo ao ponto de acreditar que somos marcados e inalteráveis por causa dos mesmos. É preciso desconstruir estes mitos, mas tal não vai acontecer com livros como este. Uma oportunidade perdida.
February 19, 2025
I don't know much about biology so this was exhausting to read; I only really made it through about six chapters and that was with a heavy amount of LLM help. It seemed important and the first few topics related to things I kind of knew in interesting ways (how genetics are more complicated than "this gene creates this protein / causes this trait"; why protein folding matters) but then it became a blur.
Some things I learned:
- Chromosomes only form the classic "X" shape when they're dividing; they're usually more tangled.
- I knew that there wasn't a single "height gene" but didn't know the scale of the complexity: 62% of most common gene variations are associated with height somehow.
- In humans, only 2% of DNA encodes proteins; the rest isn't necessarily "junk" but has other functions (such as regulating what gets transcribed when).
Some things I learned:
- Chromosomes only form the classic "X" shape when they're dividing; they're usually more tangled.
- I knew that there wasn't a single "height gene" but didn't know the scale of the complexity: 62% of most common gene variations are associated with height somehow.
- In humans, only 2% of DNA encodes proteins; the rest isn't necessarily "junk" but has other functions (such as regulating what gets transcribed when).
February 7, 2025
This was an extraordinary read! It's important for books with this much depth and complexity of heavy scientific concepts to be laid out in a common-sensical, progressive manner with terms well defined and meaningful contextual history provided. This is what Ball did, and with great skill and care for details and clarity.
I especially loved Chapter 9 on Agency. I felt like this is where Ball really pulls everything together into the narrative with higher-level meaning. Below is a summary of more important points in the entire b0ok.
Ball indicates that the biological sciences are in the midst of a revolutionary paradigm shift, from the neo-Darwinian Modern Synthesis model where natural selection at the genomic level is seen as the root of adaptive phenotypic changes, to the more coherent, cogent, and consistently-supported Extended Evolutionary Synthesis model - where emergent contextual changes on the organismal level takes place with selective information shared between multiple levels and dimensions of hierarchical organization through a highly integrated and complex set of interrelated and bidirectional processes found within the organism itself, between the organism and its' environment, and even between the organism and its' evolutionary history where selected information for that organism is imprinted and retained within its' genome.
According to Ball, these integrated processes function as multiple modes of causation to form and maintain higher levels of organization, from the cellular on up to the organism itself. And these modes of causation are cognitive in nature, resulting in agency - a holistically integrated entity that can learn and adapt in a flexibly responsive way to fluctuations within itself and its' environment by endowing it with cognitive processes of selection from a palette of behavioral variability. This agent, by its' nature, engages in meaningful actions with goal-directed behavi0rs beneficial to its' own self.
Yes, all life ascribes values and meaning and has goals! All living systems learn from experience, storing up info about their environment and using it to guide future behavior. This includes cells themselves. Cells do have agency. They have their own behavioral flexibility with their own environment within the molecular level. They communicate, cooperate and compete with each other in intricate ways, and from all this collective activity emerges a higher level and unified agency - causal emergence! Here, the agent acts as a genuine cause of change!
Ball stresses the point that agency, meaning, and purpose in this modern model of biology is not a return to vitalism where life resides within a sort of magical black box that cannot be explained. And there's no need to necessarily refer to a creator God to be responsible for creating this exquisite order from disorder.
He instead refers us to the principles linked to the 2nd law of thermodynamics along with the processes of natural selection, where agency was selected due to its efficiency and effectiveness at fighting off entropic disorder to remain in a nonequilibrium state by metabolizing and drawing from its' environment - negative entropy, whereby there is a flow from a system of high entropy to a system of low entropy. In this way, a complex agent can experience its' environment as a variety of affordances, or useful possibilities to achieve its' own goals. It is able to stave off the randomness by exerting predictive actions to influence and manipulate its' environment.
This functions to turn randomness into directional action. The agent performs a series of computations that aim to optimize the acquisition, storage and use of meaningful information. To do this, agents must construct concise representations of their world and make predictions of it.
Through this, agent are able to achieve reliably high levels of work absorption and dissipation during the process of its' formation and development.
Ball points out the striking correlation between information theory and thermodynamics - meaningful information and energy are interconvertible!
Ball emphasizes that the Darwinian account of adaptation and the thermodynamic one become one and the same! Natural selection is likely to become the route by which it acquires the ability to absorb useful energy.
"Darwinian evolution can be regarded as a specific instance of a more general physical principle governing nonequilibrium systems, whereby attunement to the environment via the formation of orderly structure facilitates energy dissipation and entropy generation."
"Life is likely to arise, purely on thermodynamic grounds, in any environment that has the necessary chemical ingredients along with concentrated reservoirs of energy. "
Biology, he insists, takes place in the "mesocosmos", which is midway between atoms and the galaxies.
So, modern biology no longer looks for meaningful answers for life from a reductive and mechanistic worldview. This gene-centric biological model does not and could not possibly explain the complexities we see.
Leaving with a great quote - one of many that can be found throughout this book:
"The requirement for evolvability needs more than replication plus mutation. It demands the existence of coherent entities, called reproducers. Such entities may be regarded as the fundamental evolvable unit of all organisms. We might crudely equate them with the cell itself. They have hierarchical organization that absorbs and adjusts to the unexpected. - the Reproducer perspective. – has the organism and its struggle for existence back at its core as it was in Darwin’s original theory. "
I especially loved Chapter 9 on Agency. I felt like this is where Ball really pulls everything together into the narrative with higher-level meaning. Below is a summary of more important points in the entire b0ok.
Ball indicates that the biological sciences are in the midst of a revolutionary paradigm shift, from the neo-Darwinian Modern Synthesis model where natural selection at the genomic level is seen as the root of adaptive phenotypic changes, to the more coherent, cogent, and consistently-supported Extended Evolutionary Synthesis model - where emergent contextual changes on the organismal level takes place with selective information shared between multiple levels and dimensions of hierarchical organization through a highly integrated and complex set of interrelated and bidirectional processes found within the organism itself, between the organism and its' environment, and even between the organism and its' evolutionary history where selected information for that organism is imprinted and retained within its' genome.
According to Ball, these integrated processes function as multiple modes of causation to form and maintain higher levels of organization, from the cellular on up to the organism itself. And these modes of causation are cognitive in nature, resulting in agency - a holistically integrated entity that can learn and adapt in a flexibly responsive way to fluctuations within itself and its' environment by endowing it with cognitive processes of selection from a palette of behavioral variability. This agent, by its' nature, engages in meaningful actions with goal-directed behavi0rs beneficial to its' own self.
Yes, all life ascribes values and meaning and has goals! All living systems learn from experience, storing up info about their environment and using it to guide future behavior. This includes cells themselves. Cells do have agency. They have their own behavioral flexibility with their own environment within the molecular level. They communicate, cooperate and compete with each other in intricate ways, and from all this collective activity emerges a higher level and unified agency - causal emergence! Here, the agent acts as a genuine cause of change!
Ball stresses the point that agency, meaning, and purpose in this modern model of biology is not a return to vitalism where life resides within a sort of magical black box that cannot be explained. And there's no need to necessarily refer to a creator God to be responsible for creating this exquisite order from disorder.
He instead refers us to the principles linked to the 2nd law of thermodynamics along with the processes of natural selection, where agency was selected due to its efficiency and effectiveness at fighting off entropic disorder to remain in a nonequilibrium state by metabolizing and drawing from its' environment - negative entropy, whereby there is a flow from a system of high entropy to a system of low entropy. In this way, a complex agent can experience its' environment as a variety of affordances, or useful possibilities to achieve its' own goals. It is able to stave off the randomness by exerting predictive actions to influence and manipulate its' environment.
This functions to turn randomness into directional action. The agent performs a series of computations that aim to optimize the acquisition, storage and use of meaningful information. To do this, agents must construct concise representations of their world and make predictions of it.
Through this, agent are able to achieve reliably high levels of work absorption and dissipation during the process of its' formation and development.
Ball points out the striking correlation between information theory and thermodynamics - meaningful information and energy are interconvertible!
Ball emphasizes that the Darwinian account of adaptation and the thermodynamic one become one and the same! Natural selection is likely to become the route by which it acquires the ability to absorb useful energy.
"Darwinian evolution can be regarded as a specific instance of a more general physical principle governing nonequilibrium systems, whereby attunement to the environment via the formation of orderly structure facilitates energy dissipation and entropy generation."
"Life is likely to arise, purely on thermodynamic grounds, in any environment that has the necessary chemical ingredients along with concentrated reservoirs of energy. "
Biology, he insists, takes place in the "mesocosmos", which is midway between atoms and the galaxies.
So, modern biology no longer looks for meaningful answers for life from a reductive and mechanistic worldview. This gene-centric biological model does not and could not possibly explain the complexities we see.
Leaving with a great quote - one of many that can be found throughout this book:
"The requirement for evolvability needs more than replication plus mutation. It demands the existence of coherent entities, called reproducers. Such entities may be regarded as the fundamental evolvable unit of all organisms. We might crudely equate them with the cell itself. They have hierarchical organization that absorbs and adjusts to the unexpected. - the Reproducer perspective. – has the organism and its struggle for existence back at its core as it was in Darwin’s original theory. "
January 16, 2024
I love reading books about science and how our world works. This is an informative and intriguing book that made me learn a lot.
I appreciated the style of writing and how easy was to understand what I was reading.
Highly recommended.
Many thanks to the publisher for this ARC, all opinions are mine
I appreciated the style of writing and how easy was to understand what I was reading.
Highly recommended.
Many thanks to the publisher for this ARC, all opinions are mine
August 11, 2025
Ütleks, et väga sisukas ja mõistlik raamat, just selle poolest, et pakkus bioloogia mõistmiseks uut perspektiivi, kuid ei väitnud ka, et senini õpitu oleks kõik vale. Autor oli oma väidete suhtes aus ning tunnistas, siis kui vaja, et ei tea kogu tõde ning et saab pakkuda vaid paremat metafoori. Samas analüüsis ta käsitletavaid teemasid hoolikalt, argumenteerides ja vastuväiteid tuues, et tõele võimalikult lähedale jõuda. Arutluskäigud olid suhteliselt jälgitavad, kuna selgitusi avas ta teiste metafooride ja paralleelide abil ning kasutas ka pilte. See oli vägagi tervitatav.
See raamat sütitas minus veelgi suurema huvi elu toimimise vastu, mis on järgnevat kolme aastat vaadeldes ainult hea. Jääb vaid loota, et ülikooli õppejõud suudavad elu komplekssust samasuguse innukuse ja detailitunnetusega selgitada. Teadmihimu on nüüd suurem, adudes, et gümnaasiumis õpitu oli pinnapealne ja kohati eksitavgi.
See raamat sütitas minus veelgi suurema huvi elu toimimise vastu, mis on järgnevat kolme aastat vaadeldes ainult hea. Jääb vaid loota, et ülikooli õppejõud suudavad elu komplekssust samasuguse innukuse ja detailitunnetusega selgitada. Teadmihimu on nüüd suurem, adudes, et gümnaasiumis õpitu oli pinnapealne ja kohati eksitavgi.
January 18, 2024
This is a fascinating book about biology in a broad sense and genetics in a more detailed view. Biotech has been developing rapidly in the past few decades so there´s a lot to catch up with. There are a lot of terms and jargon that most people probably won´t be familiar with, so those with bio/med background will enjoy this book more.
Want to read
March 3, 2024Dewey 571.8 B21h
March 31, 2024
Me gustó mucho. Un libro tal vez un poco denso para la gente que no sabe mucho de Biología, pero que entrega una nueva mirada a como entender la relación entre el genotipo y el fenotipo.
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