There are many open questions in biology, but this article is by and large the current consensus in genetics and molecular biology. There are enough facts by now that we can conclude environment plays a big role, real traits are multigenic, the lock-and-key hypothesis was misleading, and evolution has a number of tricks up its sleeve that were not previously appreciated.
Oh, if your point is that both environment and genetics (and circumstance/luck) plays a large role in development then we completely agree. If you're saying that the role of genetics is overstated or insignificant then I strongly disagree.
> Not really. They are more like incomplete recipes that depend on external factors to fill in the missing information.
As someone who has worked in construction, you have literally described blueprints.
Blueprints specify key elements of a building, what sort of material is to be used, rough locations, routing of utilities, etc, but it’s up to the installer to use their knowledge of building practices and building code to perform the installation correctly. Sometimes materials can change due to availability (or budget).
No, recipe is not the same as blueprint. As I posted just upthread, a blueprint has a lot more detailed information than a recipe.
In addition to that, a blueprint has a different kind of information. A blueprint for a human body, for example, would tell you the general plan of the body, where the organs go, how things are connected, etc. Yes, it might leave small details, like the exact location of each minor blood vessel or nerve fiber, up to the constructors, but it still is giving you an overall plan.
DNA, however, does not do anything like this. DNA information is more like (I'm giving time frames off the top of my head here, so they're probably off, but I think the general idea is correct) "at week 1 after fertilization, split into three layers; at week 3, start differentiating cell types in each layer; at week 5..." and so on. And even that information is very incomplete; it's depending on a lot of external factors to be a certain way, like blood supply from the mother, particular hormones being present at particular times in particular concentrations, etc. There is nowhere in any of that where it says "the final body in general has a head, torso, two arms, two legs, the heart goes here, the brain goes here", etc. All of those things are emergent results from the process. So much more like a recipe than a blueprint.
I think the difference (as per the article) is that what function a particular piece performs can vary wildly. A blueprint calls for a door, and there may be a lot of flexibility on which door is installed—but the builder does install a door. They don’t install a door which occasionally turns into a fireplace or blender.
> Where in the article do you see this being said?
From the article:
> This “fuzziness and imprecision” is not sloppy design, but an essential feature of protein interactions. Being disordered makes proteins “versatile communicators”, able to respond rapidly to changes in the cell, binding to different partners and transmitting different signals depending on the circumstance. For example, the protein aconitase can switch from metabolizing sugar to promoting iron intake to red blood cells when iron is scarce.
> Reality: DNA/Alleles do in fact encode the "blueprints for life".
This seems to be talking past the article, which notes: "genes’ activity — [e.g.,] the length of protein that they encode — depends on myriad external factors ... and each trait can be influenced by many genes. For instance, although the HCN4 gene encodes a protein that acts as the heart’s primary pacemaker, the heart retains its rhythm even if the gene is mutated.
> This paper is a perfect example of a process called "complicating" a field, like they tried to do with the feminist glaciology paper
Could you share an aspect of the book or a quote from the article which you think illustrates such a similarity?
I read this article twice, and I'm still not sure why it exists. It seems like a lot of flowery and vague language to basically say nothing other than "we should think about things differently because it's 2024 and old ideas are bad."
I'm now reading the book the article is reviewing. Like previous Philip Ball books, it is a dense but enjoyable read.
Like other books on genetics and biology, it is best to read it while it is still fresh: in several years time, parts of it might be obsoleted by new biological findings.
A significant amount of research output from life science labs right now is descriptive single cell RNA sequencing papers. It is perhaps the single largest present genre of basic science research, and it is sucking all the air out of the room.
I agree this article is pretty vague about criticizing this research. It doesn't name RNA sequencing.
This is tough for me. "Instead, we must let our ideas evolve as more discoveries are made in the coming decades." is a very appealing statement. My concern is admitting that something is complicated is different from saying it is not the case.
To that end, is there anyone that thinks genes are a simple blueprint for life? Seems far more accurate to say that they are part of the blueprint for life, and that even with that, we have not defined the execution environment for how that blueprint is carried out.
Do we present an even more simplified model to students? Especially young students? Absolutely. As we do to laymen. But things being markedly more complicated does not mean that models are bad.
This always confused me as well. It’s all nature in the end - your genes will react to a certain environment in a certain way. Of course we have some control over environment so it’s worth making the nature vs nurture distinction, but how you react to an environment is predetermined. Not that we can easily predict any of this given the staggering complexity.
Additionally, what’s the deal with the almost doublespeak in the article? The author plainly states that genes aren’t code, but then goes on to say they’re just more complex code.
> admitting that something is complicated is different from saying it is not the case.
I agree. I do think "too many people take convenient science metaphors as literal" is a valid concern, especially when it comes to pedagogy, but the situation is not so bad that everyone is wrong about everything. No scientist goes around thinking molecules are made of little colored plastic balls.
From meeting identical twins in my lifetime, yes I’d say they are quite a blueprint for an organism. A blueprint doesn’t mean things are exactly the same, yes there are environmental factors, but there is a lot going on there that is the same. Identical twin studies done with twins separated at birth and experiencing different environments will show you that.
Depending on what exactly you are studying, there is a much more important environment, that has dramatically different outcomes even for the same genes: the uterus you develop in. If you implanted two genetically identical fertilized eggs into two different women, you'd see a much larger difference, since the mother's body has a significant active role in controlling gene expression, one that's often forgotten about in such discussions.
And even then, it is far from clear how much of the similarity comes from the matched genes, and how much from the original egg cells having fissioned from a common ancestor, independently of the contents of the nucleus. We know the cell itself actively seeks a goal, on its own.
As that first cell divides again and again to generate the trillions of cells in your body, mutations happen in the hundreds and thousands. Even though they started with all the same genes, they certainly don't stay that way as you grow.
Isn't this a matter of semantics? A blueprint for a computer could be stored on a computer, and it's obvious that the blueprint doesn't contain everything needed to build a computer.
This is a problem with using metaphors. Blueprints very accurately describe the role of genes by the way the article here describes them. I think they don’t have a precise understanding of what blueprints are, which means now semantics of the metaphor are critiqued rather than the actual content.
You linked to an editorial about ethics. I'm not sure what to make of it, are you against conducting research and communicating it in an ethical way? Or do you disagree about something specific in that article? Either way I'm not sure I'm seeing the connection between what you're saying and the original article.
You managed to trigger multiple people. Serves as a reminder that techies often think their smarts extend to all other areas of life. I'm pretty sure there's some name for this phenomenon... :)
It doesn’t matter what time we’re in, styling scientific progress to uphold the morality of the day is inherently regressive and motivated by nothing more than the establishment trying to maintain their privilege and power.
You don’t fear research because you believe your morals and ideology are backed by facts and evidence. If we have a study tomorrow showing that day, hormone blockers have some horrible side effect that makes them an inappropriate treatment, that’s transphobic so just don’t study it. The ethics don’t matter, just everybody thinking you were on the right side of history.
The article is referring to knowledge based research ABOUT humans, not research WITH or ON humans. From the article (my capitalization added for emphasis):
---
Although academic freedom is fundamental, it is not unbounded. The same ethical considerations should underlie science ABOUT humans as apply to research WITH human participants.
...
Ensuring that ethically conducted research on individual differences and differences among human groups flourishes, and no research is discouraged simply because it may be socially or academically controversial, IS AS IMPORTANT as preventing harm. Science has for too long been complicit in perpetuating structural inequalities and discrimination in society. With this guidance, we take a step towards countering this.
---
History seems to endlessly repeat itself. Not just in broad strokes but quite literally, down to identical events and happenings. In the past the Church did actively encourage scientific research, but there was the condition that any findings and framings could not contradict the common ideological values of the time. And here we are again.
We do have studies showing this, and the research has been attacked in the way you describe. Far too many people have immersed themselves in this belief system, believing themselves to be righteous above all else, curtailing any critical thought around that topic.
It's kind of fascinating to observe once you realize what's going on, that it's a secular cult whose followers don't even notice they're trapped within.
Are you saying that organizations like the Mayo Clinic or Cleveland Clinic are ideologically captured and are suppressing information about the risks of puberty blockers?
Do you have a source for this claim? What is this secular cult and how is it trapping people?
Even better, what if someone developed a drug that simply makes gender dysphoria disappear? Those suffering of dysphoria could then choose to avoid a lengthy, painful and destructive process to align their body to their mind, and take a drug and align their mind with their body. How do you think it would be received?
It always surprising to me when people on programming related forum, a discipline that in a sense is all about viewing the world trough different levels of abstractions, get defensive when exposed to the fact that real world also do have them. Be that sociology, history or even 'hard science', simplyfing the world is inherent to comprehending it.
Now, ofcourse, there are still 'good' abstractions and bad ones.
But even the best one, by definition, hides some details away.
As for the article itself - I do agree that it is mostly a fluff, and not something revolutionary.
But also nothing to criticize it for, either
As in: based on physical one, where the perceived abstractions aren't completely arbitrary solely on the discretion of programmer, but come from some observable fact.
> This burst of activity represents a frustrated thought that “it is time to become impatient with the old view”, as Ball says. Genetics alone cannot help us to understand and treat many of the diseases that cause the biggest health-care burdens, such as schizophrenia, cardiovascular diseases and cancer.
Does anyone actually subscribe to this "old view"? Surely the majority of scientists, medical professionals, and laymen alike understand environmental factors play a huge part in this. Why make a call to action to address a imagined state of affairs?
Even in this most simplified form, it's clear genes don't determine all of the outcome. You're Y% more likely to get a disease, with other factors affecting how the dice actually fall.
I can personally attest that some medical professionals have a pretty dismal broad understanding of genetics and evolution. And besides, even if the book isn't breaking new ground, or is targeting a more a popular audience, a good writer synthesizing developments in a field and providing fresh metaphors for understanding it can be tremendously beneficial, even to the academic side, I think. There's also an element of marketing and puffery in how authors talk about their new books.
All that said, yeah. I've for a long time liked the simple idea that the organism is the product of interaction between genes and their environment. That simple notion alone banishes many of the supposed misapprehensions under attack in this article.
Some idiots (on both sides) seem to think "nature vs nurture" must have a single winner. Some slightly less stupid people like to strawman all their opponents as thinking that. This seems to be yet another example of the latter.
> Surely the majority of scientists, medical professionals, and laymen alike understand environmental factors play a huge part in this.
The majority of laypeople have no idea what you are talking about, and if they know anything, I would guess from colloquial language that they 'know' your 'genes' are inherited and determine things about you, in a way you can't change or avoid.
I'm not criticising the laypeople (or flattering us), but pointing out that we are in a bubble ... on another planet ... in a different universe ....
I expect that more scientists and medical professionals are back on planet Earth (i.e., unaware) than you imagine. Who else would the OP be targeted at?
Not sure about in the sciences, but large companies and their funders still do. e.g., 23AndMe, which still wants to become profitable through drug development based pretty much only on DNA sequencing data.
I agree with the article, it's a paradigm that peaked 20 years ago, and has been outdated for about a decade.
But I'm not being absolutely critical since I'm only viewing from the sidelines and perhaps there is still something important to be gained correlating genetics with disease for cases where there is little hope of a standard diagnosis.
> Precision Medicine, on the other hand, is an innovative approach that takes into account individual differences in people’s genes, environments, and lifestyles.
That seems to be a far cry from asserting genetic determinism. Can you explain what you were trying to communicate with that link?
A reliable career-advancing publication in the life sciences often follows the pattern: Look, everybody! We've found a genetic marker for X! Here's how we sequenced the organisms, and here are the stats we ran to identify this particular gene or constellation of genes.
This was exciting research in the 90s, but now gene sequencing is routine and the results just get added to the pile. It's scientific chum.
This book's authors, the review author, and the editors at Nature who decided this review was worth publishing and under what headline, would like to coordinate a shift away from this kind of low-impact publication.
To make significant contribution, you can't just identify a marker for cancer or dinosaurism: you need to actually attempt to cure cancer or turn people into dinosaurs.
It's not like that kind of research is value-less though. It's still important to do that kind of thing, firstly for practical purposes such map is useful, and secondly it can help with building a more fundamental theory. (The same is true of the "particle zoo" before the Standard Model was developed in Physics). I don't think stopping doing it means you'll get the big breakthrough any faster, in fact it'll slow things down.
It seems people think that, if we just focus more on Kuhn's "revolutionary science" instead of incremental, "normal science", we'll get more paradigm-shifting theories.
It could just be that paradigm-shifting breakthroughs are exponentially harder to find, and that it's not just a matter of "we just didn't look hard enough"
"We found a genetic marker for X" is even more fuzzy when talking about something like Schizophrenia or Autism, because the diagnosis itself is very far from a precise label. It's not just about missing environmental contributions or dealing with how complex interactions between different generic markers are, though these are also issues. We're averaging over probably dozens of different issues in the vast majority of studies, and that extends to other subfields of biological psychiatry too.
The article is disorienting, and it glosses over the real issues. “It's time to admit that the water is wet”, oh yes.
“The view of biology” they talk about doesn't exist. What exists is pop-science, with its acolytes and proselytes, boldly claiming that everything is as easy as 1-2-3:
1) We just make a list of All The Genes.
2) We put All The Data into the Computer.
3) We solve any problem by finding a relevant connection.
Just imagine how much nonsense was said about “genes”, from racial cleansing projects to self-help books — or reasoning why corner store closed. As we are speaking about all kinds of genealogy, it is worth mentioning that pop science is a distant cousin of real science, and is closer to 19th century militant vulgar materialism, the kind of marketplace “science” which promised that corpses would get reanimated by wondrous electricity in the same manner it made frog's leg move. “Only need to figure enough details”, as usual. Now “genes” or “evolution” are just a way for common people to talk about “fate” or “dog-eat-dog” in “scientific” terms.
With that sorted out, we can study the scientists. Unfortunately, a lot of them aren't that different from the general public in understanding that for each efficiency of some model, there is a corresponding deficiency. Educated people honestly ask why we shouldn't use computer metaphors so carelessly all the time. It's like asking why hammers can't be used for everything, or why integers exist when we can use floating point for everything (and also deliberately ignore the complexities because “we're dealing with general cases, we don't need that”). Is there something wrong with the hammer? No, there isn't, something is wrong with the people who don't really understand what they are doing.
So the book review basically says “Fine, we all know it's a pathetic circus, but it's our circus, and lots of people are trained to play their parts, so let's declare some patented nonsense outdated, do a facelift, an go on”.
Many biologists will say that studying evolution and development is the key to understanding how phenotypes arise. I agree. Watching the development of an organism- say, a tardigrade egg that grows over a few days and then hatches- is remarkably edifying.
You can see individual cells growing and moving around and then look at another tardigrade egg and see exactly the same cells growing and moving around to the same exact places (this is a feature called eutely- they have a predetermined lineage of cells all arising in the same tree structure from the same original egg cell, which (in many tardigrade species) is in fact a clone of its mother (no fathers rrequired- known as parthenogenesis).
I think many people would see that, along wiht other observations, and easily come to the conclusion that specific behaviors were encoded for by individual genes, or that genes act like an architectural blueprint, exactly specifying either intermediate or final states.
Instead, in each of those cells is a blob of jelly filled with the genome, which is decorated with all sorts of proteins that are flying around, binding to vairous specific sites, activating and deactivating other sites, which then get turned into RNA and ultimately specific proteins. These proteins execute a plan encoded in the genome, but they do so probabilistically, with noise immunity, following physical behaviors that can be understood rationally (although in most cases, the number of actual variables is far too large to work with). And that encoding is extremely complex, more like a collection of weakly linked PDEs (a lot of weakly linked PDEs).
There is massive feedback, both positive and negative, that contributes to automatic regulation of components so that the plan proceeds normally. Many of these regulations lead to extremely non-linear, complex behaviors. Yet, for all this complexity, fairly straightforward actions that are similar to tardigrades happen in nearly all life. A sphere forms from an egg. The egg splits in two cells, then four, then many, retaining the spherical shape. At some point one of the split cells develops a polarity- one side grows more actively than the other. This leads to a body development plan (https://en.wikipedia.org/wiki/Blastulation) that self-generates with mostly local interactions (IE, there's no central controlling cell, it's more that the cells are just pushing against each other and the result is the right shape).
Understanding how genotypes lead to phenotypes has been a massive journey and I have had to unlearn much of what I was originally told, as new data has subsumed previous ones. That mendelian model of peas with discrete characteristics that segregate on different chromosomes is useful, and does show up in biology, but from what I can tell, it's just an easy, special case that we saw early, then geneticists overfit new data on that model.
When viewed through evolution as well as development- we start to see how complex phenotypes begin, then evolve to become far more complex. Early eyes and wings had utility, similar to modern eyes, but far less capable. Through mutation and selection, the organisms whose eyes worked slightly better were more likely to generate offspring that inherited those properties,leading to even more radiation (into many different types of organisms that all share similar eye properties).
I used to think that by this time in my career (I'm 51), we'd have been able to address a simple question I asked when I was 18: why is my nose this funny shape that doesn't look like other people's noses? What genes "encode" the "blueprint"? And to be honest, we're still really far from answering questions like that, but through a combination of data collection and machine learning, scientists actually are beginning to understand the complex process that leads to funny nose shapes.
> we'd have been able to address a simple question I asked when I was 18: why is my nose this funny shape that doesn't look like other people's noses? What genes "encode" the "blueprint"? And to be honest, we're still really far from answering questions like that, but through a combination of data collection and machine learning, scientists actually are beginning to understand the complex process that leads to funny nose shapes.
IIRC there was some research that could predict facial shapes from genomes (but it's not a popular direction of research since it touches various taboo topics too closely for many people's comfort), and notably it does not require understanding complex process of how e.g. noses are formed, just data about sufficiently many people to detect correlation patterns.
Yes, it's been a painful lesson for me to learn: you can often build a good-enough approximation of the underlying physics to make good-enough predictions, even without modelling all the molecular details directly, as long as you have enough data, good algorithms, and fast computers.
https://www.annualreviews.org/doi/full/10.1146/annurev-genom... is a review of research in this area. I don't think it's particularly controversial because realistically, the underlying data supports the hypothesis that facial features are hereditable and then do association studies to find plausible candidate multivariate genomic features that predict them accurately. I think that's far enough from controversial "Race science" that it's hard for people to make reasonable criticisms of this research.
Of course "cells are computers and genes are their code" is an oversimplification, but it's not a terrible analogy. It seems to fail the worst if either
- you stretch the analogy too far, as is the case with all analogies, or
- you don't understand much about computers or code.
A given set of code can produce different results when compiled by different compilers, or on a different computer, or for a different computer, and a given executable can produce different results depending on whether or not libraries or peripherals are available, etc.
No one will ever be able to make a one-sentence analogy that will satisfy every scientist, but in spite of that many analogies are incredibly useful. If someone doesn't like the "cells are computers and genes are their code" analogy, I'm all ears for a better one.
I have given a few genetics talks this past year to technical groups and I start the talk by saying
"This is no more difficult to understand than any event based system" [insert image of the Netflix micro services architecture]
This gets a laugh.
DNA is like an executable file written in assembly. Most of the time it makes a bunch of pure functions (but not always) and it is self modifying, lol. For most of the work I do I can presume that gene X produces a "pure function"
At the next level up you have a bunch of functions that can take some arguments and spits out some stuff. The question is does that function work etc?
At the next level up you have systems thinking. If I have 100 lambda servers that are all executing from a queue and then I have 20 lambda servers that are all reading from those 100 you can guess where the data is going to pile up.
I am radically over simplifying, but hopefully you see the parallels to binary, code, application logic
In our "designed" software you can almost never go and change one line to modify the behavior of a program. Instead you have dozens if not millions of functions that all interact depending on the lens by which you want to look. Usually it is contained in on "area" with code that matters the most, but that isn't always the case. Is it any surprise that biology is even messier?
The article mentions the 300 genes related to schizophrenia. This is like me mentioning that my random Go service also uses a bunch of Go standard library code when it is executing.
Debugging stuff like this is what our careers are made of.
For a long time scientist were looking for a single gay gene. Poking around once I knew what to look for it only took around 6 months to figure out the whole LGBT, but in nearly all cases it involves more than just one gene. You simply have to apply debugging logic at each layer to figure it out. It is handy to understand all the layers, but depending on the problem not always required.
Wow - can you elaborate on your process to “debug” these different layers? What comprises your personal or team’s feedback loop, given that 6 months is short? (I suspect it’s a lot of sequencing?) Are there good comparisons to be made with getting acquainted with a new codebase/technical system? Are there any particular computational tools involved? Pardon all the questions, this stuff is fascinating!
To be clear this is/was a hobby project. Getting access to DNA files is required yes, but sequencing wasn't really the limiting factor. It started with simply poking around my DNA file and then some friends many of which were only done on 23andme. Most of the time was spent reading countless papers and making hypothesis, trying to invalidate them and iterating. Constantly seeking out new ways to look at the problem and going from there. Every time I got a new DNA file from someone I could see how their dna fit into the current hypothesis. Because every DNA was different it was a great way to test them. It anything it made my job easier. I wasn't looking for a single snp, but common patterns.
Sometimes this has involved using nebula and their whole genome sequencing dna test to get much more accurate data, but more often than not the cheap dna tests most people do were good enough.
As for actual programs, I did write some quick and dirty scripts to scan dna files for specific snps, but mostly I would just read them as the parts I needed were not that long.
There is a fair amount of phenotype data to start with. What ultimately started this was knowing 1) that there was a number of conditions that are seen in statistically weird numbers in the LGBT and 2) sex hormone levels in the LGBT are not exactly what you would expect.
My goto fun question when talking with someone in the LGBT is if they have hypermobility. A good percentage do. In one specific example those with classical like EDS will have 21-OHD and thus POTS and elevated 17-OHP, backdoor DHT production (aka PCOS for women) etc.
The real question I have been pondering is what exactly do I do with this as this is just a fun puzzle, not my job, I don't work for any school etc.
I don't get it. If you can solve for LGBT genes that easily, then why isn't this in the news? Surely academic scientists would have tried this if all you needed was some scripting to find patterns?
Been interviewed by a medical news journal and this has all been done in the public over the last year so there was never a “release date” or anything. Honestly at the start I was just another person with a guess.
There are some scary implications such as in some cases we have had sexuality and gender changes once we knew how to “inject into the system”
I guess when you get down to it, it wasn’t actually that note worthy by itself as most cases are simply minor versions of already well documented conditions. It is only when you combine them that they add up.
And lastly given that I have not paid to get it peer reviewed and published formally it isn’t news yet. Again no school affiliation. Just now mostly helping treat a bunch of those common conditions I mentioned.
There has been some research mostly into gay men. But honestly the transgender data set is much richer. At the end of the day it is a minority that is being politicized so not exactly being investigated, but once you figure it out it is like shooting fish in a barrel there is so much easy research. Before this it was (simplifying but not) brain scans for the most part. It was mostly unknown.
I know of Sapolsky saying what a decade ago that LGBT brain structures are, like, flipped wrt. heterosexual people. But I thought the scientific consensus has been that there is no easy way to find a gay gene(s), so your claim of finding such low-hanging fruit seems to fly in the face of that. I'm already imagining that academic scientists would be ready to dismiss your work outright.
Why didn't the medical news journal hook you up with a professor? They could've taken a look at your work. Like, how do you know your scripts isn't just doing pseudoscience and based on a superficial understanding of all those papers, especially if this is just a hobby project. There could be blind spots.
I am already working with a doctor and have talked with those in academia. They find it neat, but are not going to jump projects, they already have their area of study that they are working to publishing something on, not this.
There absolutely could be blind spots and been iterating on it all year each time the tweaks are smaller, but the core idea has not changed, but simply accumulated more and more evidence.
Consensus is that there is no single "flip this and you're gay" gene, but we've known for decades there is a genetic component because of twin studies. Fits right up with what this person says they've found.
If we're allowed to use computing analogies here, would it be fair to say the old model is more like how we view a standard CPU and the new model is more like a FPGA? Where the old model viewed genes in a more classic reductionist approach as CPUs, arranged and static logic waiting for input from the environment and impressing on the environment in such a deterministic way. While the newer model analogy, genes act as an FPGA, an array of gates with potential to adapt to input imposed upon them with this bi-directional synchronicity of environment impressing on genes and genes therefore impressing on environment?
It seems as fields mature we move further away from classic reductionism and encompass more a holistic approach, a path gravitating towards objectivity which I find interesting from a philosophical perspective.
For those old enough to program on punch cards you could say that is closer. We load the program into ram and then the env can and often does modify the program on the fly and we do dumb thing like use the current line number to save a byte because dividing by 17 is “good enough”. Most cards are functional and many cards do double or triple duty to save space. So a bug in one card can subtly break three wildly different spots. Analogies break down of course as in biology it all executes at the same time which is why the micro services or lamdas that can be scaled up or down have been my go to. And you can even inject external events into your lambda systems.
And for anyone familiar with lisp, code is data, data is code. For modern coders you can think that it has a billion feature flags you can also flip on and off rather than rewriting the code on the fly
I recall a simplification that said that if we used computers code as an analogy, genes would be similar to functions, epigenetics would be similar to conditions over which functions get called and when, and the environment is the argument and events in which the program get executed with.
Like genes, the following collections of information are plans, as other entities (workers, compilers, cells, etc) can reliably use them to produce larger, more complex objects:
- Blueprint
- Instruction manual
- Recipe
- Code
Unlike genes, they’re all human-designed. The top-down forcing function - the “back” in the feedback loop which shapes them - is human artifice.
I’ll leave it as an “exercise to the reader” to consider the differences in how their environment and execution apparatuses affect the resulting objects.
Genes are like blueprints, but obviously not the same. For one, they haven’t passed the county permitting process! And living organisms are like buildings because you can point to the plan behind them. But I’ll be darned if a house has ever had to struggle for survival.
I still find the analogy mostly appropriate. Perhaps, it is not the 'high level source code' that is strictly typed as was perhaps believed by some, but I think it can still act as analogous to the runtime memory state of the computer. The genes are like memory mapped services which can operate on one another and change their state, and this couples with interrupts from the external environment that force changes to the state and memory, but the runtime code adapts and still has access to in-memory functions to call when appropriate, but every so often a buffer overflow can occur or be enticed and this causes other issues.
Yea, you have to keep in mind that while it's sort-of code, it's code written by random errors and selection. Obviously the code quality isn't going to be awesome :P
The article's title and the words of Denis Noble are quite incendiary and come across as misinformed. Are the non-quoted ideas attributable to Ball accurate? I don't know.
The actual quotes from Ball, wherein he laments the comparisons of cells to computers comes across as ill-informed. Computers operate on programs. If a program is dependent on complex state, includes random factors, error correcting codes, etc., how is it incompatible with the description of the cell?
Yes, cells are immensely complex. But that does not preclude analogizing to a computer.
This critique strikes me as refusing to admit the nuance of another's argument while demanding others see the "correct" nuance in one's own.
I have not read the book, but the article makes it sounds like the author thinks most scientists or laypeople are stuck in their views from the sixties, seventies, and eighties, which in my experience is unbelievably far from where scientists in academia and drug discovery stand for the last couple of decades at least. Of course it is useful to know the human genome and to study genetics more broadly, as it is to know about simplifying assumptions like a rigid protein conformation. In physics, the harmonic oscillators are a central unifying concept and yet they don’t appear in the real world so nobody stops their quest for truth at the harmonic approximation. Cells are complex machinery with many unknown pieces in them despite our best efforts to decipher them. Maybe the computer analogy to cells is not bad, however one has to think of this computer as made of floppy, flexible, self modifying pieces that exchange information and materials with their environment as they compute, and not think about your typical nanolithography or UV laser etched silicone-based chips.
I don't know, I think a lot of final products don't come out that close to the blueprint to begin with, or don't stay that way for long once put to use.
It's how things are expected to be constructed, but expectations are not always realized.
This is totally different from any design stage that is iterative or modular in that way though.
It’s more like that laminar flow demo where you mix the paints in a circle and then unmix them the other way - the patterns are there but the way they emerge cannot be understood due to chaos and complexity.
The story is something like this: the genes act out in an environment. They encode information which demonstrably makes the most important and obvious differences between, say, a fruit fly and human. However, they don't necessarily encode all of the cellular environment in which they act. (Though do direct its activity and proliferation.) That environment is part and parcel of life as much as the genes.
The cellular structure is maintained and propagated by the DNA. If you want to say that the very first cell’s structures (the zygote) is inherited from the mother and not produced by the individual’s genes but by the mother’s genes I suppose you could define that first cells organelles as a special kind of gene ‘inherited’ from the mother, but it certainly is not what people mean by the environment in discussions about nurture vs nature.
That's why I said "cellular environment". The literal biological environment in which genes act. Not the household environment in which a human baby finds itself; that's indeed something else. But I'm saying that genes are not the complete blueprint of life even in this "low level" sense. (Never mind that gene expression is in the developed individual is subject to external factors, too).
The interesting part is that what we call disordered is really likely to be something more akin to organized chaos in some or even many cases. Sure it is not an helix or a sheet that is all nice and tidy (and yet there are a lot of variation there as well).
A bit of the same with the "junk-DNA".
It reminds me a bit when unexperienced developpers join a team, they often want to get rid of what seem useless to them and "simplify".
Saying genes are not the blueprint for life is for me like saying “physics can not predict our life”. It cannot but everybody knows physics is the foundation of our universe. However, our world is ways to complex to use physics laws to predict all aspects of it. Stochastic is the intrinsic nature of every complex system.
That is exactly the wrong model. Genes are only a part of how your body is formed, and two identical genotypes will not produce identical phenotypes if the environment, especially the very very early environment of the egg/uterus, is different. That's why we can't grow babys in vats, for example, and are having massive issues even trying to grow tissues in vitro (and growing whole organs is not even a dream for now).
Consider also that your neurons, your red blood cells, your muscle cells, your liver cells, your fat cells etc all have the exact same genes. And yet, they are vastly different between each other, and you'll never see a fat cell divide into a red blood cell and a neuron, even though they are "built of the same blueprints".
> Genes are only a part of how your body is formed
And blueprints are only a part of how a house is formed. Two different teams of workers can build very different houses from the same blueprint. So what you say here sounds just like a blueprint, I don't see why that is wrong.
Edit:
> Consider also that your neurons, your red blood cells, your muscle cells, your liver cells, your fat cells etc all have the exact same genes. And yet, they are vastly different between each other, and you'll never see a fat cell divide into a red blood cell and a neuron, even though they are "built of the same blueprints".
Yes, and us programmers tend to deploy the same code to many different servers and tell some of them to be databases, others be frontend etc. It is just simpler and more robust to share code and then then just flip a few settings on startup to change what the server is.
A single blueprint describing many things that are working together and you can build any of those things is very common.
My understanding is that "outside of the genes information" is not just the color or the shape of the house, it is _essential_ instruction on how to build the house. Without it, you will not get something that qualifies as "house".
In the analogy, it is not 2 teams that build houses that are very different, it is two teams that use the same blueprint and one ends up with a house, and the other one ends up with a car. In this case, it is then correct that the "blueprint" is in fact not a blueprint.
Or another way of seeing it, you have the blueprint of the house, then you rip it apart in small pieces. Some of these pieces are the genes, other of these pieces are "out of the genes", such that if you just have the genes pieces, you just don't have enough information to build something that qualifies as a house. (funnily enough, you can say that the house builder can "fill the gaps" with his own knowledge, which would be a good example of "out of the genes" instructions)
As for your software analogy, again, some software have flags to turn between databases or frontend. But the point of the article is to explain that it is demonstrable that genes don't correspond to that: genes in itself are not enough to make blood cells by just turning a flag on or off, the same way a piece of wood is not a blueprint of both a chair and a door and that the carpenter is just a simple flag that will turn the piece of wood into a chair or a door. In this software analogy, it's like if you have one script file that just contains one basic function that neither does a database or a frontend. If you combine this script with other software pieces, you can have a database, if you combine this script with other software pieces, you can have a frontend.
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[ 3.2 ms ] story [ 317 ms ] threadhttps://en.wikipedia.org/wiki/Epigenetics
Not really. They are more like incomplete recipes that depend on external factors to fill in the missing information.
However, this has been known for decades and is not a new discovery. So I agree that this article is not describing any kind of breakthrough.
As someone who has worked in construction, you have literally described blueprints.
Blueprints specify key elements of a building, what sort of material is to be used, rough locations, routing of utilities, etc, but it’s up to the installer to use their knowledge of building practices and building code to perform the installation correctly. Sometimes materials can change due to availability (or budget).
In addition to that, a blueprint has a different kind of information. A blueprint for a human body, for example, would tell you the general plan of the body, where the organs go, how things are connected, etc. Yes, it might leave small details, like the exact location of each minor blood vessel or nerve fiber, up to the constructors, but it still is giving you an overall plan.
DNA, however, does not do anything like this. DNA information is more like (I'm giving time frames off the top of my head here, so they're probably off, but I think the general idea is correct) "at week 1 after fertilization, split into three layers; at week 3, start differentiating cell types in each layer; at week 5..." and so on. And even that information is very incomplete; it's depending on a lot of external factors to be a certain way, like blood supply from the mother, particular hormones being present at particular times in particular concentrations, etc. There is nowhere in any of that where it says "the final body in general has a head, torso, two arms, two legs, the heart goes here, the brain goes here", etc. All of those things are emergent results from the process. So much more like a recipe than a blueprint.
Well I disagree with this, but it's a useless discussion to have.
Where in the article do you see this being said?
From the article:
> This “fuzziness and imprecision” is not sloppy design, but an essential feature of protein interactions. Being disordered makes proteins “versatile communicators”, able to respond rapidly to changes in the cell, binding to different partners and transmitting different signals depending on the circumstance. For example, the protein aconitase can switch from metabolizing sugar to promoting iron intake to red blood cells when iron is scarce.
(Emphasis added by me)
I do agree with the idea of changing the goalposts in the above article because as you mentioned DNA do in fact encode the "blueprints for life".
This seems to be talking past the article, which notes: "genes’ activity — [e.g.,] the length of protein that they encode — depends on myriad external factors ... and each trait can be influenced by many genes. For instance, although the HCN4 gene encodes a protein that acts as the heart’s primary pacemaker, the heart retains its rhythm even if the gene is mutated.
> This paper is a perfect example of a process called "complicating" a field, like they tried to do with the feminist glaciology paper
Could you share an aspect of the book or a quote from the article which you think illustrates such a similarity?
Like other books on genetics and biology, it is best to read it while it is still fresh: in several years time, parts of it might be obsoleted by new biological findings.
It’s a review of a book.
I agree this article is pretty vague about criticizing this research. It doesn't name RNA sequencing.
To that end, is there anyone that thinks genes are a simple blueprint for life? Seems far more accurate to say that they are part of the blueprint for life, and that even with that, we have not defined the execution environment for how that blueprint is carried out.
Do we present an even more simplified model to students? Especially young students? Absolutely. As we do to laymen. But things being markedly more complicated does not mean that models are bad.
Additionally, what’s the deal with the almost doublespeak in the article? The author plainly states that genes aren’t code, but then goes on to say they’re just more complex code.
I agree. I do think "too many people take convenient science metaphors as literal" is a valid concern, especially when it comes to pedagogy, but the situation is not so bad that everyone is wrong about everything. No scientist goes around thinking molecules are made of little colored plastic balls.
https://www.gu.se/en/gnc/what-have-twin-studies-taught-us-ab...
As that first cell divides again and again to generate the trillions of cells in your body, mutations happen in the hundreds and thousands. Even though they started with all the same genes, they certainly don't stay that way as you grow.
Still, I stand by it, as I do not believe there is merit in earnestly engaging with people who feel it's inappropriate to condemn racism and sexism.
You don’t fear research because you believe your morals and ideology are backed by facts and evidence. If we have a study tomorrow showing that day, hormone blockers have some horrible side effect that makes them an inappropriate treatment, that’s transphobic so just don’t study it. The ethics don’t matter, just everybody thinking you were on the right side of history.
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Although academic freedom is fundamental, it is not unbounded. The same ethical considerations should underlie science ABOUT humans as apply to research WITH human participants.
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Ensuring that ethically conducted research on individual differences and differences among human groups flourishes, and no research is discouraged simply because it may be socially or academically controversial, IS AS IMPORTANT as preventing harm. Science has for too long been complicit in perpetuating structural inequalities and discrimination in society. With this guidance, we take a step towards countering this.
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History seems to endlessly repeat itself. Not just in broad strokes but quite literally, down to identical events and happenings. In the past the Church did actively encourage scientific research, but there was the condition that any findings and framings could not contradict the common ideological values of the time. And here we are again.
It's kind of fascinating to observe once you realize what's going on, that it's a secular cult whose followers don't even notice they're trapped within.
Do you have a source for this claim? What is this secular cult and how is it trapping people?
See also: https://unherd.com/2024/02/why-did-three-journals-reject-my-...
The title of the article you linked to: “Science must respect the dignity and rights of all humans”
Hmm, yes, I can see why you might find that troubling. Can’t have scientists go around respecting people, that’s just madness.
Pravda means Truth, Comrade.
Now, ofcourse, there are still 'good' abstractions and bad ones. But even the best one, by definition, hides some details away.
As for the article itself - I do agree that it is mostly a fluff, and not something revolutionary. But also nothing to criticize it for, either
Does anyone actually subscribe to this "old view"? Surely the majority of scientists, medical professionals, and laymen alike understand environmental factors play a huge part in this. Why make a call to action to address a imagined state of affairs?
I think that’s how genetics is communicated… if you have gene X, you’re Y% more likely to get a disease. Stuff like that.
All that said, yeah. I've for a long time liked the simple idea that the organism is the product of interaction between genes and their environment. That simple notion alone banishes many of the supposed misapprehensions under attack in this article.
Because it's easier to argue against windmills than actual opponents.
because writing a science book is a career-influencing milestone?
The majority of laypeople have no idea what you are talking about, and if they know anything, I would guess from colloquial language that they 'know' your 'genes' are inherited and determine things about you, in a way you can't change or avoid.
I'm not criticising the laypeople (or flattering us), but pointing out that we are in a bubble ... on another planet ... in a different universe ....
I expect that more scientists and medical professionals are back on planet Earth (i.e., unaware) than you imagine. Who else would the OP be targeted at?
I agree with the article, it's a paradigm that peaked 20 years ago, and has been outdated for about a decade.
But I'm not being absolutely critical since I'm only viewing from the sidelines and perhaps there is still something important to be gained correlating genetics with disease for cases where there is little hope of a standard diagnosis.
That seems to be a far cry from asserting genetic determinism. Can you explain what you were trying to communicate with that link?
Among the general population? It absolutely is.
This was exciting research in the 90s, but now gene sequencing is routine and the results just get added to the pile. It's scientific chum.
This book's authors, the review author, and the editors at Nature who decided this review was worth publishing and under what headline, would like to coordinate a shift away from this kind of low-impact publication.
To make significant contribution, you can't just identify a marker for cancer or dinosaurism: you need to actually attempt to cure cancer or turn people into dinosaurs.
It could just be that paradigm-shifting breakthroughs are exponentially harder to find, and that it's not just a matter of "we just didn't look hard enough"
“The view of biology” they talk about doesn't exist. What exists is pop-science, with its acolytes and proselytes, boldly claiming that everything is as easy as 1-2-3:
1) We just make a list of All The Genes.
2) We put All The Data into the Computer.
3) We solve any problem by finding a relevant connection.
Just imagine how much nonsense was said about “genes”, from racial cleansing projects to self-help books — or reasoning why corner store closed. As we are speaking about all kinds of genealogy, it is worth mentioning that pop science is a distant cousin of real science, and is closer to 19th century militant vulgar materialism, the kind of marketplace “science” which promised that corpses would get reanimated by wondrous electricity in the same manner it made frog's leg move. “Only need to figure enough details”, as usual. Now “genes” or “evolution” are just a way for common people to talk about “fate” or “dog-eat-dog” in “scientific” terms.
With that sorted out, we can study the scientists. Unfortunately, a lot of them aren't that different from the general public in understanding that for each efficiency of some model, there is a corresponding deficiency. Educated people honestly ask why we shouldn't use computer metaphors so carelessly all the time. It's like asking why hammers can't be used for everything, or why integers exist when we can use floating point for everything (and also deliberately ignore the complexities because “we're dealing with general cases, we don't need that”). Is there something wrong with the hammer? No, there isn't, something is wrong with the people who don't really understand what they are doing.
So the book review basically says “Fine, we all know it's a pathetic circus, but it's our circus, and lots of people are trained to play their parts, so let's declare some patented nonsense outdated, do a facelift, an go on”.
You can see individual cells growing and moving around and then look at another tardigrade egg and see exactly the same cells growing and moving around to the same exact places (this is a feature called eutely- they have a predetermined lineage of cells all arising in the same tree structure from the same original egg cell, which (in many tardigrade species) is in fact a clone of its mother (no fathers rrequired- known as parthenogenesis).
I think many people would see that, along wiht other observations, and easily come to the conclusion that specific behaviors were encoded for by individual genes, or that genes act like an architectural blueprint, exactly specifying either intermediate or final states.
Instead, in each of those cells is a blob of jelly filled with the genome, which is decorated with all sorts of proteins that are flying around, binding to vairous specific sites, activating and deactivating other sites, which then get turned into RNA and ultimately specific proteins. These proteins execute a plan encoded in the genome, but they do so probabilistically, with noise immunity, following physical behaviors that can be understood rationally (although in most cases, the number of actual variables is far too large to work with). And that encoding is extremely complex, more like a collection of weakly linked PDEs (a lot of weakly linked PDEs).
There is massive feedback, both positive and negative, that contributes to automatic regulation of components so that the plan proceeds normally. Many of these regulations lead to extremely non-linear, complex behaviors. Yet, for all this complexity, fairly straightforward actions that are similar to tardigrades happen in nearly all life. A sphere forms from an egg. The egg splits in two cells, then four, then many, retaining the spherical shape. At some point one of the split cells develops a polarity- one side grows more actively than the other. This leads to a body development plan (https://en.wikipedia.org/wiki/Blastulation) that self-generates with mostly local interactions (IE, there's no central controlling cell, it's more that the cells are just pushing against each other and the result is the right shape).
Understanding how genotypes lead to phenotypes has been a massive journey and I have had to unlearn much of what I was originally told, as new data has subsumed previous ones. That mendelian model of peas with discrete characteristics that segregate on different chromosomes is useful, and does show up in biology, but from what I can tell, it's just an easy, special case that we saw early, then geneticists overfit new data on that model.
When viewed through evolution as well as development- we start to see how complex phenotypes begin, then evolve to become far more complex. Early eyes and wings had utility, similar to modern eyes, but far less capable. Through mutation and selection, the organisms whose eyes worked slightly better were more likely to generate offspring that inherited those properties,leading to even more radiation (into many different types of organisms that all share similar eye properties).
I used to think that by this time in my career (I'm 51), we'd have been able to address a simple question I asked when I was 18: why is my nose this funny shape that doesn't look like other people's noses? What genes "encode" the "blueprint"? And to be honest, we're still really far from answering questions like that, but through a combination of data collection and machine learning, scientists actually are beginning to understand the complex process that leads to funny nose shapes.
For those who ...
IIRC there was some research that could predict facial shapes from genomes (but it's not a popular direction of research since it touches various taboo topics too closely for many people's comfort), and notably it does not require understanding complex process of how e.g. noses are formed, just data about sufficiently many people to detect correlation patterns.
https://www.annualreviews.org/doi/full/10.1146/annurev-genom... is a review of research in this area. I don't think it's particularly controversial because realistically, the underlying data supports the hypothesis that facial features are hereditable and then do association studies to find plausible candidate multivariate genomic features that predict them accurately. I think that's far enough from controversial "Race science" that it's hard for people to make reasonable criticisms of this research.
- you stretch the analogy too far, as is the case with all analogies, or
- you don't understand much about computers or code.
A given set of code can produce different results when compiled by different compilers, or on a different computer, or for a different computer, and a given executable can produce different results depending on whether or not libraries or peripherals are available, etc.
No one will ever be able to make a one-sentence analogy that will satisfy every scientist, but in spite of that many analogies are incredibly useful. If someone doesn't like the "cells are computers and genes are their code" analogy, I'm all ears for a better one.
"This is no more difficult to understand than any event based system" [insert image of the Netflix micro services architecture]
This gets a laugh.
DNA is like an executable file written in assembly. Most of the time it makes a bunch of pure functions (but not always) and it is self modifying, lol. For most of the work I do I can presume that gene X produces a "pure function"
At the next level up you have a bunch of functions that can take some arguments and spits out some stuff. The question is does that function work etc?
At the next level up you have systems thinking. If I have 100 lambda servers that are all executing from a queue and then I have 20 lambda servers that are all reading from those 100 you can guess where the data is going to pile up.
I am radically over simplifying, but hopefully you see the parallels to binary, code, application logic
In our "designed" software you can almost never go and change one line to modify the behavior of a program. Instead you have dozens if not millions of functions that all interact depending on the lens by which you want to look. Usually it is contained in on "area" with code that matters the most, but that isn't always the case. Is it any surprise that biology is even messier?
The article mentions the 300 genes related to schizophrenia. This is like me mentioning that my random Go service also uses a bunch of Go standard library code when it is executing.
Debugging stuff like this is what our careers are made of.
For a long time scientist were looking for a single gay gene. Poking around once I knew what to look for it only took around 6 months to figure out the whole LGBT, but in nearly all cases it involves more than just one gene. You simply have to apply debugging logic at each layer to figure it out. It is handy to understand all the layers, but depending on the problem not always required.
Sometimes this has involved using nebula and their whole genome sequencing dna test to get much more accurate data, but more often than not the cheap dna tests most people do were good enough.
As for actual programs, I did write some quick and dirty scripts to scan dna files for specific snps, but mostly I would just read them as the parts I needed were not that long.
There is a fair amount of phenotype data to start with. What ultimately started this was knowing 1) that there was a number of conditions that are seen in statistically weird numbers in the LGBT and 2) sex hormone levels in the LGBT are not exactly what you would expect.
My goto fun question when talking with someone in the LGBT is if they have hypermobility. A good percentage do. In one specific example those with classical like EDS will have 21-OHD and thus POTS and elevated 17-OHP, backdoor DHT production (aka PCOS for women) etc.
The real question I have been pondering is what exactly do I do with this as this is just a fun puzzle, not my job, I don't work for any school etc.
everyone loves a good story.
Whatever you do, maybe do it anonymously?
It really sounds like it could badly trigger many people who will viciously attack others, actively attempt to destroy their lives, etc.
Be careful? :)
There are some scary implications such as in some cases we have had sexuality and gender changes once we knew how to “inject into the system”
I guess when you get down to it, it wasn’t actually that note worthy by itself as most cases are simply minor versions of already well documented conditions. It is only when you combine them that they add up.
And lastly given that I have not paid to get it peer reviewed and published formally it isn’t news yet. Again no school affiliation. Just now mostly helping treat a bunch of those common conditions I mentioned.
There absolutely could be blind spots and been iterating on it all year each time the tweaks are smaller, but the core idea has not changed, but simply accumulated more and more evidence.
It seems as fields mature we move further away from classic reductionism and encompass more a holistic approach, a path gravitating towards objectivity which I find interesting from a philosophical perspective.
And for anyone familiar with lisp, code is data, data is code. For modern coders you can think that it has a billion feature flags you can also flip on and off rather than rewriting the code on the fly
Everyone arguing DNA isn't code, its just a reductive metaphor, and that the computer analogy is wrong, don't understand computers/code, or DNA.
There is such a 1-1 correspondence, that the 'metaphor' begins to look more 'real'.
Like genes, the following collections of information are plans, as other entities (workers, compilers, cells, etc) can reliably use them to produce larger, more complex objects:
- Blueprint
- Instruction manual
- Recipe
- Code
Unlike genes, they’re all human-designed. The top-down forcing function - the “back” in the feedback loop which shapes them - is human artifice.
I’ll leave it as an “exercise to the reader” to consider the differences in how their environment and execution apparatuses affect the resulting objects.
Genes are like blueprints, but obviously not the same. For one, they haven’t passed the county permitting process! And living organisms are like buildings because you can point to the plan behind them. But I’ll be darned if a house has ever had to struggle for survival.
The actual quotes from Ball, wherein he laments the comparisons of cells to computers comes across as ill-informed. Computers operate on programs. If a program is dependent on complex state, includes random factors, error correcting codes, etc., how is it incompatible with the description of the cell?
Yes, cells are immensely complex. But that does not preclude analogizing to a computer.
This critique strikes me as refusing to admit the nuance of another's argument while demanding others see the "correct" nuance in one's own.
It's how things are expected to be constructed, but expectations are not always realized.
It’s more like that laminar flow demo where you mix the paints in a circle and then unmix them the other way - the patterns are there but the way they emerge cannot be understood due to chaos and complexity.
It reminds me a bit when unexperienced developpers join a team, they often want to get rid of what seem useless to them and "simplify".
Consider also that your neurons, your red blood cells, your muscle cells, your liver cells, your fat cells etc all have the exact same genes. And yet, they are vastly different between each other, and you'll never see a fat cell divide into a red blood cell and a neuron, even though they are "built of the same blueprints".
And blueprints are only a part of how a house is formed. Two different teams of workers can build very different houses from the same blueprint. So what you say here sounds just like a blueprint, I don't see why that is wrong.
Edit:
> Consider also that your neurons, your red blood cells, your muscle cells, your liver cells, your fat cells etc all have the exact same genes. And yet, they are vastly different between each other, and you'll never see a fat cell divide into a red blood cell and a neuron, even though they are "built of the same blueprints".
Yes, and us programmers tend to deploy the same code to many different servers and tell some of them to be databases, others be frontend etc. It is just simpler and more robust to share code and then then just flip a few settings on startup to change what the server is.
A single blueprint describing many things that are working together and you can build any of those things is very common.
In the analogy, it is not 2 teams that build houses that are very different, it is two teams that use the same blueprint and one ends up with a house, and the other one ends up with a car. In this case, it is then correct that the "blueprint" is in fact not a blueprint.
Or another way of seeing it, you have the blueprint of the house, then you rip it apart in small pieces. Some of these pieces are the genes, other of these pieces are "out of the genes", such that if you just have the genes pieces, you just don't have enough information to build something that qualifies as a house. (funnily enough, you can say that the house builder can "fill the gaps" with his own knowledge, which would be a good example of "out of the genes" instructions)
As for your software analogy, again, some software have flags to turn between databases or frontend. But the point of the article is to explain that it is demonstrable that genes don't correspond to that: genes in itself are not enough to make blood cells by just turning a flag on or off, the same way a piece of wood is not a blueprint of both a chair and a door and that the carpenter is just a simple flag that will turn the piece of wood into a chair or a door. In this software analogy, it's like if you have one script file that just contains one basic function that neither does a database or a frontend. If you combine this script with other software pieces, you can have a database, if you combine this script with other software pieces, you can have a frontend.
https://www.astralcodexten.com/p/its-fair-to-describe-schizo...
I just wish he’d apply the same reasoning to his believes on the genetics of intelligence.