This brings up a question for me. Does brain size always correlate to intelligence? I see a dolphin brain that looks very human and I think that it does, but then I see how smart crows are and I'd honestly say that they're smarter than my dog in most ways.
"Does brain size always correlate to intelligence?"
Not really, otherwise whales and elephants would be way smarter, than us.
Well, some people say, they are, but it does not show in our intelligence tests.
And birds brains evolved differently than those of mammals, so maybe they are more efficient with their relative small brain? Because yeah, they are definitely smarter than dogs, who have a bigger brain.
Maybe whales are "smarter" than us. How can we empirically test whale intelligence? Their technological abilities are obviously inferior, but I wouldn't be surprised if they were surprisingly intelligent in other ways. I'm trumpet dumb, that doesn't mean I'm not "overall smarter" or "niche smarter" than some people who play trumpet.
“For instance, on the planet Earth, man had always assumed that he was more intelligent than dolphins because he had achieved so much—the wheel, New York, wars and so on—whilst all the dolphins had ever done was muck about in the water having a good time. But conversely, the dolphins had always believed that they were far more intelligent than man—for precisely the same reasons.” - Douglas Adams
This quote is always in the back of my head anytime brain size or intelligence is discussed, and is especially when dolphins are mentioned. And, he has a point.
But apparently the dolphins in hitchhikers guide to the galaxy did a bit more, than just having a good time in the water - because unlike the humans, they managed to find a way to leave the earth, when it was destroyed. (Book 4)
And this is not further explained in the book, but it likely sounds like technology. And when you want to have and use technology, you have to do more than just splashing around..
Since dolphins evolved a couple of times, they might had that tech lying around just in case. The point stands, dolphins use their tech so they can muck about in the water. Humans to compete in a rat race and for survival in its essence. Which come to think of it, is absolutely absurd if for any intelligent species. So we aren’t that smart.
Well, when you consider that we react to global crisis like a pandemic with more confrontation, than cooperation (there was no real exchange of technology between west and east and patents and licencing were still more important, than producing enough vaccines) and to the climate crisis rather with more wars over whats left of the ressources, than to unite and solve the problems - no, we are not.
We are smart enough to see, what could be possible, but unable to overcome primitive power struggles.
Well, do you really think humanity as its whole acted "smart" during the pandemic?
And cherrypicking, well climate change is the current problem, affecting the whole earth, so a smart species by my definition would act globally and coordinated and not only talk about it. But sure, by comparison we still seem to be the smartest around.
> Not really, otherwise whales and elephants would be way smarter, than us.
How do you know that? I mentioned this in another comment, but dolphins and orcas have more folds in their brain than we do, and folding is associated with greater processing power and higher function. Additionally, the areas of their and whales' brains associated with emotional intelligence are much larger relative to the rest of their brain than the same areas in our brain are. Their brains are very, very interesting. For example, they keep one brain hemisphere active during sleep since they are conscious breathers, and they actually alternate which hemisphere is kept awake.
Whales, dolphins, and orcas are damn smart, and I think there's evidence enough that we cannot conclude that they aren't more intelligent than us. Although they lack technological development, this is due to their living environment and physiobiology and not due to their intelligence. Orcas in particular have achieved complete dominance of their environment, aside from human activity, and are geographically widespread with diverse cultures. There are many cases where orcas actually use humans as tools, even training humans to help them in hunts (and not the other way around).
Sorry to be crass but I'd assume intelligence is somewhat correlated with mastery of the physical world (I mean if it weren't we wouldn't care about things like AI alignment) and while cetaceans are clever mammals they're not very good at avoiding being soup. I sympathize with them, but if they were "way smarter than us" we would be running and hiding instead of debating how nicely we should treat them.
I already addressed that though. Operating under the hypothetical and assumption that humans could survive in the ocean, humans couldn't develop technology and written history and knowledge in the ocean without having done so on land first, even with our hand dexterity, much less with fins.
Humans existed a long time before proper technology development, and those humans were just as intelligent as modern ones. The ability to create technology is not a requirement for higher intelligence.
Even then, orcas do use tools, what they have access to. Without technology, humans stand no chance against an orca, and that goes for any animal in the ocean, from blue whales to great white sharks.
You’re implying something is only showing intelligence if it shows complexity (long linguistic demonstrations here)
Isn’t it more intelligence to convey all the information that you need to with the highest efficiency?
We rate a poet who can convey tremendous meaning in few lines as superior to someone who is long winded and their writing is full of bullshit and tropes conveying nothing but using many words.
I’m suggesting that increasing complexity and nuance present in a substrate such as language is a prerequisite for high intelligence because high intelligence in individuals is a feature of groups, not individuals.
One person alone is without language and without advanced tools, no matter how big their brains. See feral children.
It is possible that cetaceans pushed long ago pushed past complex verbosity into communication via wisdom and are all enlightened beings. Maybe they communicate electrically. Maybe they are in a local maximum of telepathic connection. I hope so.
> Then we should expect cetaceans to have developed long verbal/oral lineages
Why? But nonetheless, they have. They pass on locations, routes, hunting techniques, etc. vocally and behaviorally down through generations.
You and some of the other comments bring up a lot of things that don’t really have much to do with intelligence. They really only have anything to do with a human-centric view of intelligence.
If you cannot build and communicate abstract concepts collectively your ability to select evolutionarily for
increased capacity for abstract concepts seems to me to be very limited. I am all for different forms of intelligence, but at least attempt to define it and how it comes about.
>Humans existed a long time before proper technology development, and those humans were just as intelligent as modern ones. The ability to create technology is not a requirement for higher intelligence.
Is that actually true? In cases of feral or severely neglected children who lack any exposure to human language, isn't there an impediment that prevents them learning more complex language later in life that exceeds anything that could be attributed to reduced brain development due to nutrition?
World wide hasn't intelligence been increasing, and while part of that is due to better nutrition, another part is due to better childhood conditions to enable intelligence? Exposures to the technology of language, written language, and similar at a young age seem to lead to an increased capacity for intelligence later in life.
Isn’t it true? Hominids and Homo sapiens were around millions and hundreds of thousands of years, respectively, before technology more advanced than basic tools showed up. And written history seems even shorter than that.
I’m not for sure what feral or neglected children has to do with this.
To address your later point, intelligence does not equal knowledge. Any increase in intelligence in a person’s life seems to be intralifetime and doesn’t spill over to further generations. Increasing intelligence through diet and behaviors and such are just mechanisms for exposing the underlying intelligence that’s already there.
>To address your later point, intelligence does not equal knowledge.
This is just one of the many paths to the fundamental question that plagues this sort of topic, what is intelligence. Is intelligence the capacity for gaining knowledge or having actually gained knowledge? Or maybe not directly related to knowledge at all, though the previous question was more about the capacity to gain vs the gaining than it was about knowledge.
It is known that the capacity a single individual changes based on what they were exposed to (feral/neglected children being the extreme negative cases, I'm not as well read on extreme positive cases). But perhaps we aren't talking about an individua's capacity and instead we are talking some baseline genetic average capacity for a larger group that doesn't take into account environmental cases pushing it to either extreme? But in such a case have we not defined intelligence so that technology's impact is excluded a priori?
that's an assumption that more intelligence means that they would have to be motivated by revenge and vengeance as opposed to that being a distinctly human flaw
This is a good point, and it reminds me of something. I do wonder if the ability to be content is a sign of higher intelligence. Humans are decidedly discontented, and I can't help but be curious about that being a possible showcase of our ignorance.
I do not know it. I am not an expert and had only limited, (but fascinating) contact with them.
But I would assume, if they would be "way smarter", than they could and would find ways of communicating with us. As far as I know, the research shows that they can communcicate towards each other quite well, but not towards us beyond very basic things.
But of course that reminds me of an old joke:
A donkey and a dog on a farm are talking to each other in the evening and the donkey complains that he has so much work to do, but would like to become a writer. The dog asks: why don't you tell the farmer? The donkey answers, are you crazy? If he finds out, I can read and write, I will also have to do his bookkeeping.
Meaning, maybe whales and co. could communicate with us, but choose not to.
But if this would be the case, their reasoning would have to include some very astonishing things, as whales are still hunted - which they likely could almost completely stop by telling us exactly that.
> But I would assume, if they would be "way smarter", than they could and would find ways of communicating with us. As far as I know, the research shows that they can communcicate towards each other quite well, but not towards us beyond very basic things.
That’s a human centric approach and a little strange, because how do we communicate with them? We can’t understand them or communicate with them any more than they can with us.
Old Tom was an orca off the Australian coast who, with his pod, trained humans on how to efficiently catch whales. Old Tom demanded the tongues of the whales, which was given to him by the whalers.
> Whales, dolphins, and orcas are damn smart, and I think there's evidence enough that we cannot conclude that they aren't more intelligent than us.
Where's this evidence?
What exactly does "more intelligent" mean to you? Do you think a dolphin can learn to play e.g. Chess? I doubt you can teach them to play even tic-tac-toe.
Birds have a higher neuron density. Each neuron is a mini Turing machine running on DNA instructions so they could also have better instinctual software.
Cells perform a staggering number of parallel computations. Neurons are cells, and perform these same calculations and more in addition to emitting spikes. Spikes, rather than being the major form of computation, appear instead to be a means of maintaining synchronization.
I quite honestly did not think of it this way. But it makes some sense. I always thought cells perform, for lack of a better term, self-maintenance operations independently from their macro function (the receiving and emitting of spikes, in this case). I did not think of the internal operations of a cell being connected to the macro function in any sophisticated or meaningful way. I would love to inform myself better on this topic since it is not by area of expertise, and I have an admittedly cursory understanding.
I do think the field of psychopharmacology is probably sufficient to give an appreciation of the complexity involved at the same time as being useful to the practical understanding of how medications (and food) change behavior. It's also well studied and there are good books. I think Dr Stahl's books are the university standard. Like a lot of science though I think much of it is 'current best guess'.
For information on the modifying DNA expression in neurons that's under epigenetics and not as well studied.
That simplifies neurons a bit too much. There are a variety of neuron types including mirror neurons and pyramid neurons. These can feature more or less branching even.
neurons have gates, these gates interconnect and form logic networks.
these are histeretic, programable, and dynamic.
the neuronal body state, the electro-osmotic environment, the past history of state are primary effectors of structure,and function resultant in the logic.
You are correct. Neurons are not Turing machines. However, they are complex enough that they can be Turing machines so it can be fun to call them that.
I didn’t expect this topic to be so controversial to be honest. I’m not surprised though.
I fully admit I may be underinformed. I had thought, though, that neurons were not sophisticated in the way a Turing machine is and much more akin to memristors. However, that may be a memristor tinted view of the world.
Neurons definitely compute. The dendrites that aggregate signals to initiate an action potential are not just simple summations but complex arrangements of signal promoters and inhibitors. The complexity of a pyramidal neuron is equivalent to a 5-8 layer artificial NN.
And that result is just from a computer simulation of a neuron that focuses on the dendrites and doesn't appear to extensively model the nucleus.
"Unfortunately, it’s currently impossible for neuroscientists to record the full input-output function of a real neuron, so there’s likely more going on that the model of a biological neuron isn’t capturing. In other words, real neurons might be even more complex."
This makes no sense in the way neurons work as far as I understand it. RNA 'instructions' are processed by the Ribosome to make proteins, it isn't software in a machine code sense but more of molecular specification for a piece of material to be produced.
I only downvoted you because "each neuron is a mini Turing machine running on DNA instructions" isn't a very helpful observation except at the most abstract level.
In my extensive research of neurons (as an independent/citizen scientist) it looks like the closest analogy to me. Neuron behavior is not only mediated by DNA but neurons can also write changes back into DNA, not to mention the nucleus soup that acts a bit like registers. I work on small molecule peptide medicine that changes gene expression in the neurons and other to glia cells to treat medical conditions.
This isn't even wrong. Seriously, if you want to do science get educated, your statements on this subject ("I should add that I've taken to do my own research because I little faith in the actual scientists to do a good job, and the faith that I have left is diminishing.") make me discard your output as 'likely noise' rather than signal. If you want to be taken seriously then you should make a minimal effort to try to understand what it is that you are talking about, as it is you come across as a kook and that likely isn't your intention.
I don’t work alone, I do work with scientists who I think are good. When I speak in generalizations it is just that a generalization. Science has been subtly redefined from a methodology to ‘what a scientist does’ and scientists these days produce papers.
I don't like your phrasing this as the need to attack something unfactual or not, and it's not 'other matters' it is precisely this matter: to come up with stuff that goes against established science in a way that makes it difficult, if not impossible to argue with.
The general field is Epigenetics (gene expression based on environment), and within that there is research on how peptides act as modulators by silencing and un-silencing different genes. You can get a list of known bioactive peptides by reading it from the DNA or by using mass spectrometry (there’s a proper name for this but it escapes me atm). So putting the two together you can have quite a bit of external control over gene expression.
I’m not involved in the process of acquiring the ‘omics data. I just analyze it and read papers from other people analyzing it. I think MALDI-TOF is the gold standard for proteomics.
Even if it's self-modifying, can continue state, etc, the Turing machine analogy is a bit of a stretch. And the current mainstream considers the primary function of neurons to be their information-transmitting capability, rather than their self-modifying ability.
Don't let my negative attitude keep you from doing research- I just think that epigenetics has been a bit overblown as a functional mechanism, or its just too hard to prove anything useful with experiments. Personally, if I was working on this I'd focus much more on neural differentiation during neurogenesis, rather than self-modification during "runtime".
I’m aware of how attractive the information-transmitting analogy is given the elegance of the theory. A few simple rules when combined form an infinitely complex emergent behavior able to sufficiently explain all observations; what’s not to love about it.
I’m focusing on the epigenetic aspect of neurons due the possibility of the ME/CFS/LongCovid family of conditions being due to silencing of certain genes. The brain is closely linked with the immune system and I think the so while these present as immune conditions I believe it starts out more as a neural condition, maybe microglia. In addition it makes sense to focus on this area more as I can’t consciously restructure the neurons in my brain but I can introduce peptides that change gene expressions.
I haven't yet read the main article at that link, but its opening links to another long blogpost on whatbuywhy.com about the human brain and it's fascinating! Highly recommended: https://waitbutwhy.com/2017/04/neuralink.html
Dogs have been bred for docility not intelligence. Their wild cousins, wolves, are considerably more intelligent, they’re just prone to get bored and engage in undesirable behaviors. I’m told that it’s very easy to teach a tame wolf tricks, but they quickly lose interest in obviously pointless activities, especially as they mature.
It is possible that the selective processes that led to ”modern” brains are essentially a process of self-domestication, and certain “diagnoses” are just reflections of diversity in that process.
If society collapsed I think it would be more beneficial to be ADHD than not.
Not them but just guessing... that most ADHD traits are only 'disordered' if you expect humans to be able to sit still, shut up, and focus exclusively on what you tell them to focus on for 8 hours a day?
If there's a weak correlation in a population, finding no correlation in some subpopulations and a stronger correlation in others is expected.
For example, a very weak correlation between GPA and job performance exists. In some disciplines, like law, the correlation is strong. In other fields, like extreme medicine, there is no correlation.
No, this was meant to be an intuitive example of weak correlation. It could have been about a correlation between the redness of a fruit and its sweetness. For the entire population of fruit, it is weakly correlated. For some apples, it is strongly correlated. And for tomatoes, there is no correlation.
Extreme medicine, which includes field, mountain, and battlefield medicine, is a specialization of general medicine. You can study it as a part of various programs. I studied it as a specialization in a general practitioner's MSc program in Central Europe. Depending on the region, it is probably possible to specialize in extreme medicine as a nurse or an EMT.
There was a wide range of GPAs in that program because success was measured by a narrow range of criteria that did not include things usually considered "academic aptitude" - mainly the ability to follow resuscitation algorithms in simulations precisely. Some of the things we were scored by automatically were time to ECG, time to defibrillation, correct callouts to the team, intubation depth and time, and chest compression depth and rate. And failing to execute a particular algorithm meant immediate failure. Every other imperfection immediately meant a reduced score, and scoring was entirely metric-based in simulators, not open to human interpretation.
Scoring just 45% of the possible grade on tests was considered excellent. You had to demonstrate very high competency to pass. Mediocre knowledge of algorithms or skills in resuscitation was unacceptable because that would severely worsen the outcomes of actual patients.
If you either cared about your GPA or were primarily motivated by your GPA at school or university, it was clear that this would be a very difficult specialization for you. It was more for people who excelled in algorithm following, composure under stress, and perseverance; and those who wanted a high skill ceiling.
you are suggesting that "caring about GPA" is what leads to high GPA. That's like suggesting that "caring about scoring stats" is the key to what leads athletes to accumulate high scoring stats.
Certainly. Students who care about their GPA will put more effort into maintaining a high one. I am not claiming it is the only GPA determining factor.
Twins should be the ultimate check in whether head size actually means anything (otherwise it could just as easily be nutrition, sleep, or other factors that generally lead to growth).
> twins should be the ultimate check in whether head size actually means anything (otherwise it could just as easily be nutrition, sleep, or other factors that generally lead to growth)
Twins are great for ruling out genetic factors. It may still be the case that neonatal nutrition drives both head size and adult IQ.
It's a solved question. Of course brain size relates to intelligence, albeit noisily. What, why do people assume that the increase in brain volume in the evolutionary record, concurrent with the increase in sophistication of material culture, doesn't set a prior for within-species effects of variance in this trait? Do we have another computational substrate besides brain contents? Would this skepticism be considered reasonable in the context of any other tissue and its quantifiable function, like muscle or bone?
This is the most up-to-date meta-analysis on the topic:
> Brain size and IQ associations yielded r = 0.24, with the strongest effects observed for more g-loaded tests and in healthy samples that generalize across participant sex and age bands.
Not necessarily faster, but you definitely have way more leg power.
Various hypotheses on how a larger brain is actually used to control a larger body and thus doesn't translate into specific "brain power" usable for intelligent activities are unsound.
I’ve read there’s decent correlation on a few scientific journals on Google scholar. Namely, that while head size doesn’t guarantee intelligence, if you are predisposed to intelligence you can’t be as smart as someone else who is predisposed to intelligence but has a larger head.
No because the structure and function of the organ is at least as important as the size. Size (or rather some bound of neuron/glial count + complexity) is more in the necessary-but-not-sufficient category.
Secondly the question is not well-posed enough to answer accurately. What is intelligence, in this case?
The cytoarchitecture of brain parcels/regions varies significantly. If you have a giant cerebellum you are not going to seem very smart to us, but you may have a very large brain. At the other end, people have lived normal (if perhaps internally simpler) lives with tiny fractions of a typical neocortex. [0]
Larger animals tend to have larger brains than smaller animals. If you divide the actual brain size of an animal by the size of brain an average animal that size would have, you get the "encephalization quotient". If you rank some common animals by encephalization quotient, most of the resulting order probably isn't surprising to many people:
1 In a meta-analysis, Deaner et al. (2007) tested ABS, cortex size, cortex-to-brain ratio, EQ, and corrected relative brain size (cRBS) against global cognitive capacities. They have found that, after normalization, only ABS and neocortex size showed significant correlation to cognitive abilities.
2 The notion that encephalization quotient corresponds to intelligence has been disputed by Roth and Dicke (2012). They consider the absolute [number of cortical neurons] and [neural connections]as better correlates of cognitive ability.[[16]](https://en.m.wikipedia.org/wiki/Encephalization_quotient#cit...)
One idea I've proposed for this is that is mostly correlation and just a little causation. Like assume going bigger is in an easy to get a little bit smarter, but at a large energy cost. Then EQ measures how willing the animal is to invest in additional smarts. If it's willing to invest energy, then it will also mean that evolution will favor intelligent animals more strongly so it will evolve other ways of becoming smarter than just going bigger. Perhaps more faster or more efficient neurons or better mactro structure. And those other things are where the major benefits come from.
well a bigger brain requires a bigger head requires a bigger body to carry it, so this would seem to push the chances of higher intelligence onto the animals with the bigger bodies. But I'd guess it is just a slight increase in the likelihood, since the structure is probably of more importance.
If you assume some sensor density, along the body, is required, then a larger body means more sensory cells, which necessitates more nerves, which requires more neurons to make sense of them in a meaningful way.
Interestingly, the biggest bird of all, the ostrich, might also be the dumbest. Or at least ostriches are in the conversation with pigeons and turkeys.
Probably this is because the ostrich doesn't need to be as intelligent. No flight, big clumsy beak etc. And they can avoid predation just by being huge and kicking really hard.
City birds like crows and pigeons have puzzles they can play with like getting food out of garbage bins and so on. City birds tend to be more intelligent than countryside birds, even within the same species.
I always felt like cats are actually smarter than dogs in a lot of ways. Dogs have a lot of their brain power dedicated to manipulating and communicating with humans, as well as trainability. But untrained dogs just seem kinda stupid and helpless to me whereas cats can learn to be almost completely independent with next to no training. Dogs are evolved from pack animals of course which explains a lot of this.
Last link has a formula to calculate cranial volume.
Animal intelligence is vastly underplayed. Ants seem to be a very intelligent creature but they're little more than part of nature to us. We're similarly adapted to our environment, and those animals are adapted to our patterns and mentation by virtue of millennia of close contact / purposeful genetic pushes (eg, dogs)
Dinosaurs had their chance and they lost, but I'm slightly terrified of the idea of a crow scaled up to the size of a chimpanzee, and I actually like corvids (though not as much as some). There are raptors roughly that size, so it's not impossible, unlike scaling an ant to the size of a crow, which would only give you a paperweight made out of chitin.
They clearly have a different 'instructions per cycle' ratio from mammal brains.
Brain size has more to do with body size than anything. Most of your brain functions as a motor control and sensory processing center. To willfully move muscle in your body, requires brain power. This is why after a stroke, and a part of your brain dies, you can lose both the ability to move sections of your body, along with feeling anything in those sections.
As so, larger animals have bigger bodies, and hence typically have bigger brains in order to handle/control their larger bodies.
I'd be extremely interested, because good biological foundation for intelligence doesn't necessary leads to advanced thinking. Size + internal structure + context.
I remember several years ago reading about "junk DNA" or "useless DNA" in sequences. Even then, I was certain that it probably wasn't "junk", we were just yet to understand it. I wish we'd take that attitude a bit more with science journalism. "It doesn't make sense..... YET".
That was born of the widely held metaphysical position that evolution is purposeless. Given that assumption one would expect to find plenty of “junk” DNA.
If the primary goal is survival based primarily on efficient use of energy. A lot of evolution is about organisms becoming more efficient by adapting to their environment. So then keeping unnecessary junk around is inefficient and we would expect orgasms that lose to would benefit and out breed the others.
Having our optic nerve run right through our retina producing a blind spot in order to capture an upside down and backwards image is pretty inefficient too. Evolution doesn't maximize efficiency, it maximizes good-enough-to-reproduce-ity.
Better adapted organisms are just that - better. Not perfect, or free of inefficiencies. And even a perfectly adapted organism might not be as good at adapting to changes in the very long term compared to one with "junk" DNA. Also, does unused junk in the DNA really hurt energy efficiency?
There are parts that are almost certainly not under functional selection and provide no benefit whatsoever- with Alu sequences being the best candidate. Even in tthe case of Alu, they do seem to have some vague effect on regulation of transcription... although they're not what we would call "genes" or "regulatory regions".
In other cases, there are just lots and lots of duplicates of the same genes over and over. Other parts appear to be forges of gene creation- either through gene duplication and divergent evolution, or through some other mysterious mechanism we don't know yet.
Certainly, we've had parts that looked like they were nothing at all and ended up being very important, and other parts that looked like they were incredibly important, but were really just the side effect of some effective parasite.
It's sort of not even an interesting debate any more, as most of the initial positions everybody held were changed when we interrogated more, and better data.
There are also fairly strict limits, given human mutation and reproductive rates, on the amount of information that can be preserved in the genome. Most of the genome is therefore meaningless (although not necessarily useless). As this article points out, these regions allow for random creation of novel proteins
Even for the “no benefit whatsoever” parts, is it not possible that they influence (and are possibly crucial to) the rest of the system just by providing spacing between other more-apparently-functional parts?
I’m thinking by analogy of executable programs that have runs of zeros. The zeros don’t necessarily do anything, but remove them and everything else is out of alignment.
I am open to the idea that "boring duplicated regions" performance some vague function through spacing. Some folks have proposed doing experiments where the spacers are removed, or replaced with other sequences, but they are extremely hard experiments to properly do (in a way that convinces the field).
We already know that enhancers "work at a distance" and it's not clear what "distance" exactly means, and it gets into complicated 3D structure of the genome inside a cell; see https://en.wikipedia.org/wiki/Enhancer_(genetics)
Personally I think that the best way to think about the genome is to unlearn most of the preconceptions you learned in genetics and instead think about it in terms of biophysics and development and machine learning: you'll never realyl be able to understand the true function of every little bit, but you cvan probably create an approximate model that explains the vast majority of biology with relatively few variables, and some deep models that contain all the necessary statistics to model these systems accurately.
It sounds like because there is a very complex 3D structure that the 'spacing' function could actually be extremely important. Far more so than zeros in machine code.
I love the analogy. Many times I think about the genome as a bunch of machine code it's my job to reverse engineer. That was a good part of my career- probably 20 years- before I realized the problem was that it's much too hard to actually "prove" anything about systems like genomes.
That object code has been heavily modified during runtime for billions of years. We have no access to the original source code for any of the patches, though at this point it would be incomprehensible anyway.
This link dives quite deep into what is an ALU, for those interested.
ALU elements: Know the SINEs [short interspersed elements]
Alu elements are primate-specific repeats and comprise 11% of the human genome. They have wide-ranging influences on gene expression. Their contribution to genome evolution, gene regulation and disease is reviewed.
"Junk DNA" brought to you by the same geniuses that brought you "we only use 10% of our brain cells" and "the heart is where the spirit resides, the brain is just useless grey goo."
I'm not sure where I encountered this hypothesis but I find it compelling. As noted by many, junk DNA, acquired from viruses and mutations and genome shuffling, is quite a puzzle. Why does it persist? It takes energy to copy, and misreading it can cause fatal or maladaptive mutations. From that perspective, it shouldn't persist (with slowly accumulating drift) for billions of years, as some shared junk sequences have across species. But it does.
Obviously, because it isn't junk; it is of value to the organism. Even if it's not of any use right now, even if it's completely biologically inactive at present. Because it is still extremely high entropy information. They're remnants of solutions other living systems once used, at some point, to solve the problem of staying alive.
If I were going to try and exploit genetic mutation to produce novel solutions to biological problems, I would start from an existing genome. In fact, I'd start with as much data, from as many organisms, as I could get my hands on and store. Perhaps we carry junk DNA because mutations in existing coded sequences, even mutated, currently useless ones, are far more likely to be functional, and so potentially a useful adaptation, than literal randomness. It's life's portfolio of solutions, badly photocopied little snippets accumulated over the years, and we all carry it around for future generations that might live in an environment where it's useful.
> It takes energy to copy, and misreading it can cause fatal or maladaptive mutations
Can maladaptive mutations really be caused by copying DNA that's not used much (as far as we can tell, like the DNA for endogenous retroviruses in our genome)?
From the perspective of the gene it makes sense - genes that are more sucesful at making offspring (aka getting copied) should be expected to prosper through natural selection.
You must have selective pressure on genome size for organisms to evolve mechanisms to reduce the "junk". The metabolic cost of carrying around the junk is small. The cost of cleaning up the junk comes from much more frequent accidental deletions/truncations of important sequences. Upending that equation requires massive selective pressure for a smaller genome - maybe something like a tardigrade that gets desiccated regularly? In any case no chance any vertebrate species would have that kind of pressure. You'd need insane offspring counts and short generation cycles to afford the selective pressure price.
The fact that we can tap junk at some future point is probbly just an accidental side-effect... though there is another theory that claims having lots of junk provides some protection against environmentally-induced damage because most of the time it is a junk section that gets damaged. Hows that for the next error protection algorithm: pad the message with mostly zeros so occasional bit corruption doesn't matter. Take that Shannon!
If you want a specific example of this mechanism working: primate 3-color vision. In our two color blue-yellow seeing ancestors the yellow pigment sequence got duplicated, then eventually slightly mutated. That's why the red and green receptors overlap so much yet blue is standing way off by itself. It is high likely this started as a useless duplication and was carried around for a long time before one of the duplicates got mutated.
For folks interested in understanding the subject of junk DNA a bit better, there's an upcoming book [1] that might be worth checking out. The authors blog seems also to be interesting on this and related subjects.
Non-coding sequences have been understood as having some functions at least since the early 1990s. Because genome expression is dynamic, tracking the exact mechanisms of action of these sequences is challenging.
> The tragedy of a species becoming unfit for life by overevolving one ability is not confined to humankind. Thus it is thought, for instance, that certain deer in paleontological times succumbed as they acquired overly-heavy horns. The mutations must be considered blind, they work, are thrown forth, without any contact of interest with their environment.
> In depressive states, the mind may be seen in the image of such an antler, in all its fantastic splendour pinning its bearer to the ground.
"Human gene linked to bigger brains was born from seemingly useless DNA"
Considering how we've managed to use those bigger brains, that DNA still seems useless.
It would be interesting to use seemingly unused DNA to express genes. But I also wonder if these truly lack a function, or if we just don't know the function.
I've always suspected the junk DNA is where the morphogenetic algorithms are kept. Published science just doesn't know how to decode most of morphogenesis for now.
DNA specifies proteins, anatomy is not there. Something much more interesting must be going on [1].
[1] Morphogenesis as a Model for Computation and Basal Cognition by Michael Levin https://www.youtube.com/watch?v=ZW73LgOM5Bw (Where is Anatomical Information Specified - from 7:30 onwards)
Sorry for being cryptic. Mr. Levin uses this metaphor [1]: just as in the 1950s in order to change the state of a computer you would have to physically change the wires, in a proportional manner, today, when we play with genes we try to alter state at a hardware level, and from the past 70+ years of software development we simply know there is a better way to control state. Imagine you'd have to pull a soldering iron each time you wanted to switch between Adobe Photoshop and Microsoft Word, to paraphrase Mr. Levin's remark.
Therefore, there might not be any morphological secret in the DNA, junk or not: DNA encodes a recipe for the building tools to be used in the eventuality of development. Imagine I would extract the exact state of the transistors from my computer, a ridiculously long string of 0s and 1s. Which strings of 0s and 1s codify this very textbox, its background color, the position of the cursor, the cursor itself? The questions are simply at the wrong level of abstraction, even if of course the state of the textbox is certainly somewhere in that string, but if I wanted to alter state at this wrong level then I would have to move very carefully a lot of 0s and 1s, in a very particular manner, with almost no room for errors, in order to add a simple "a" character to this very textbox. Isn't it much more simple and much more interesting, in the waterfall of effects through the abstraction layers if not in action, to push the key "A" on the keyboard? The question then becomes what is and how do we press the keyboard to alter the morphospace location of a cell, a tissue, an organism. A possible answer researched by Mr. Levin's group is voltage-gated ion channels controlling bioelectrical gradients [2].
Of course, at the lowest level, we are all stardust, a collection of femtoevents between femtoparticles, but we simply do not have to operate at that level to understand and control biology: biology itself has done the work, for at least the past 4+ billions of years of evolution, to increase the level of abstraction, from bonds between carbon and sulfur [3], to rotary motors to store and transfer energy [4], to organisms capable of running some kind of simulation of the world in which their reflected self becomes an agent in the world which sometimes knows they are an agent.
You know a lot about this. Although I think gradients are mechanism of how a body implements shape, I don't think they are (nor contain) the design.
I understand your computer analogy, but I think it's misapplied because the opaque string of 01s requiring exquisite manipulation is exactly like what DNA was before we had modern genetic engineering, CRISPR, etc. And we walked the path your analogy suggests is ridiculous and impossible, to arrive with the contemporary genetic tools we now have.
I think "junk" is morphogenetics (and more), just in a different language that published science does not yet understand.
Falling back again to the research done by Levin lab, they are able to shape 2-headed or 2-tailed flatworms by altering electric potential differences, and these flatworms have the same DNA as the regular one head, one tail flatworm [1]. See them in video [2].
One other lesson to be learned from the planarian flatworms is that their DNA is a complete mess, yet they are able to fully regenerate without any issues, and are functionally immortal, they do not age [3].
DNA is certainly important and interesting and needs more research, my initial comment just pointed out that if DNA is a "CAD model", the computational layer, the basal cognition in cell/tissue/organ(ism), is even more enticing, and probably we don't even need to alter genes in order to shape morphology, giving another analogy, if a pocket calculator "knows" what 5 + 7 is, we probably don't need to build another pocket calculator just to compute 6 + 8.
We actually do know that, proteins which control expression of other genes handle the morphology. There's a gene for a left side, for example.
But the relevant thing is, they control expression by binding to pieces of non-coding DNA, which can be considered "junk" by strict definitions. So most genes are prepended by a block of if-statements.
Morphology. Shape of things. How we get arms etc. We don't know how to engineer genetics to produce desired shapes. In the 'junk' that's where the secret is...not covered by most of the current published research in gene expression...and nothing like traditional gene expression (rna transcription -> protein + signaling). Currently published science basically knows nothing about how to get shape from DNA
Imagine you're the proverbial alien tasked with introducing sentient life on Earth without arising much suspicion. Replacing useless DNA with de novo genes (of high correlation) would likely be your favorite approach.
Whereas I'm not even sure that a million of generations is sufficient to evolve new genes from scratch (i.e. not via duplication or fixing)
‘Junk’ or ‘useless’ DNA is such silly nomenclature, because obviously we will learn more in the unlimited future, and we know so little about biology now that proclaiming anything useless is short-sighted to the max.
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