One common objection to the theory of evolution claims that the theory is self contradictory. It says that it is impossible for complex features such as wings, eyes etc to evolve because they will require a series of mutations that do not individually confer any evolutionary advantage. Since they do not have any evolutionary advantage, they cannot spread in the population. Therefore the chance of these mutations appearing in series is almost as small as these mutations appearing simultaneously. The chance of these mutations appearing simultaneously is, of course, astronomically small.
The usual counterargument says that just one mutation is usually enough to create a functional prototype of a complex feature/organ (MVP, if you please). A series of mutations is not required.
This study provides yet another example backing this counterargument. One single mutation can change an unicellular entity and make it behave like a multi cellular organism. Intuitively, one would think this would take many mutations. However, intuition is wrong in this case, and in many others.
I'm a math biology (in other words, I use math to model biology problems) student, and not an evolution nay-sayer, and...the scientific work isn't at all about showing how the amazingly (I'm a student, I learn to respect my opponent) complex phenomena underlying the emergence of organs can be neatly associated with single events.
In particular, this article was of interest to me simply because of how grand a claim it makes.
In general, grand claims are something to approach with skepticism, because of laws of probability number 35, which states that: "few complex non-linear phenomena have a beautifully simple explanation, and if a grand claim purports to be such an explanation, then it most likely is not such an explanation".
It is worth reading law 36 of probability as well: "the maker of a grand claim is more likely to be a 'journalist' or a PR department person, than a scientist".
How do the laws of probability hold up? Pretty darn well, I'd say.
Here's the abstract (by the way, eLife IS an open source journal, so the journalist had no excuse here):
> To form and maintain organized tissues, multicellular organisms orient their mitotic spindles relative to neighboring cells. A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues. Here we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism. The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID. This change revealed and repurposed an ancient molecular surface that previously had a radically different function. We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals.
Key takeaways:
1) "A molecular complex scaffolded by the GK protein-interaction domain (GKPID) mediates spindle orientation in diverse animal taxa by linking microtubule motor proteins to a marker protein on the cell cortex localized by external cues"
Explanation: in this sentence, the scientists are carefully pointing out where the 'thing' (a protein domain) they are going to make a claim about fits into the biological picture. No, there isn't one superhero -- there's a carefully choreographed concert that their 'thing' is a part of.
2) "we illuminate how this complex evolved and commandeered control of spindle orientation from a more ancient mechanism"
Very cool. Simple statement. Interesting, but no grand claim.
3) "The complex was assembled through a series of molecular exploitation events, one of which – the evolution of GKPID’s capacity to bind the cortical marker protein – can be recapitulated by reintroducing a single historical substitution into the reconstructed ancestral GKPID."
Again, they reiterate how there was actually a bunch of things happening ("a series of molecular exploitation events"), ONE of which is the cool one they want to talk about.
4) "This change revealed and repurposed an ancient molecular surface that previously had a radically different function."
If you were wondering what's cool, this is what's cool.
5) In conclusion: "We show how the physical simplicity of this binding interface enabled the evolution of a new protein function now essential to the biological complexity of many animals."
Hmm...no grand claim finishing claim made regarding how this ONE thing changed EVERYTHING. Again, we are reminded of the whole picture: "so yeah guys, here's how this protein function, which is essential (because it's part of a super complex dance number) for so many living things, probably came about".
I'm going to go commission a gold filigree copy of the laws of probability.
Thanks for looking into the original document and providing a detailed explanation. You are basically saying that the journalists sensationalized the findings. The researchers do not claim that they traced the most ancient mutation responsible for multicellularity. The researchers also do not claim that this single mutation created an almost functional multicellular organism.
Am I getting this right?
Mind you, the scientists still can't entirely stop themselves from making somewhat grandiose claims:
“That’s a very different paradigm for thinking about diseases like cancer,” Prehoda said. “It could allow us to think about new ways to develop therapies by focusing on genes that are involved in this unicellular to multi-cellular process.”
Indeed, the old local maxima problem. Why doesn't evolution get stuck in local maxima; what pushes it out of those valleys and into the mountains? Why have all our evolution simulations gotten stuck?
Luckily machine learning came along and has shown empirically that the solution is to increase the number of dimensions. Our tiny neural nets of the 90s also got stuck in local maxima. But when we could finally make huge and deep networks, the problem more or less disappeared.
I believe this is the real solution to the local maxima problem in evolution. Real evolution works with a massive number of parameters, which means exploration of the problem space doesn't get stuck in local maxima, just as it doesn't in Deep Learning. When the number of tweakable parameters outstrips the dimensionality of the problem space then there is always some angle pointing up out of the valleys.
This is a different, and I think more general way of expressing the typical counterargument which you explained. "There is always some angle pointing up" is a more general way of saying "just one mutation is usually enough to create a functional prototype".
Is there any compelling reason to believe evolution _doesn't_ get stuck in local optima? It's not my field, so may be missing something obvious, but I see no reason that evolution requires complete avoidance of local optima. Different species could be the result of being "pulled" towards to different local optima. Local optima could disrupt evolution but, over time, a single large enough mutation or large enough change in external environment will either push you out of that optima, or stop it from being an optima.
Cephalopod eyes are better than mammalian ones. They evolved independently, but cephalopods ended up with an arguably "better" solution, and mammals aren't about to swap their eyes around entirely given that their eyes work just fine, even with a blindspot.
> In vertebrate eyes, the nerve fibers route before the retina, blocking some light and creating a blind spot where the fibers pass through the retina. In cephalopod eyes, the nerve fibers route behind the retina, and do not block light or disrupt the retina.
Evolution most certainly DOES get stuck in local maxima: http://m.youtube.com/watch?v=cO1a1Ek-HD0 . Also, it's quite easy for me to imagine an animal like an angel, with arms and wings. Tetrapods only have 4 limbs to work with though. For bats to gain wings they had to lose their front legs.
One obvious local sticking point is mammalian cervical vertebrae (a couple critters have more or fewer, but basically you're stuck at 7 whether you're a rat or giraffe)
> Luckily machine learning came along and has shown empirically that the solution is to increase the number of dimensions.
Ah yes, that's just what brilliant scientists like Mendel, Darwin, Fisher, Wright, Watson et al. were missing: Deep Learning! /s. The number of local optima grows exponentially in problem dimension, so increasing the dimension simply provides an even stronger guarantee that your optimizer will converge to one. Evolution, for its part, is definitely stuck in one, as evidenced by the fact that I cannot fly.
It is true there are more local minima, but they're generally pretty equivalent. In fact, in high dimensions, saddle points are a much bigger problem than local minima. [0] The fact that optimization works on these large, non-convex problems is kind of a marvel, and raises really interesting questions. (mostly "this shouldn't work this well unless there's some kind of regularity to these problems that makes them nicely behaved"). What this says about evolution I neither know nor care to speculate (above my pay grade).
> The number of local optima grows exponentially in problem dimension, so increasing the dimension simply provides an even stronger guarantee that your optimizer will converge to one.
Forgive my potential ignorance, but it seems to me that there's a difference between the dimensionality of a problem and the dimensionality of a neural net working on the problem. Did you mean to imply that adding more dimensions to a neural net increases the number of local maxima for the problem?
> Evolution, for its part, is definitely stuck in one, as evidenced by the fact that I cannot fly.
Flying requires a large number of biological tweaks that are not necessarily good for every organism. For instance, lower bone density. When humans have this, we call it osteoporosis and it's generally a Bad Thing(tm).
Also, I could argue that evolution has done a better job than you give it credit for, considering that I don't know any other animal that can travel over land at sustained high speeds, fly at extreme altitude, swim to extreme depths, and burrow through mountains.
I think a simpler explanation for why evolution doesn't get stuck in local maxima is because the environment on earth hasn't been static. Resources get depleted, animals migrate to different habitats, mass extinctions occur, competitors enter and leave, etc. All of these change the balance of which genes aid survival at any given time and make a mutation that might have bad at one point good and vice versa.
I don't understand the comparison with the neural nets of the 90s and deep learning today. There was _human intelligence_ operating on the transition between these two technologies. How does evolution compare to this?
(honest question, because I probably didn't get the angle and problem space thing)
It's not about the design of the network, it's about the training. Optimizing the weights of a DNN is a non convex optimization problem solved using gradient based search for weights that minimize a loss function. If you can only search in 10 dimensions, it's harder to move in the correct direction. Once you're searching in 1000 directions, you can usually find a path that gets you to the right place. Think of it this way: there may exist a 10 dimensional solution, but it requires learning a very dense solution.
The single largest difference is simply the size of the networks. We are tossing billions of times more processing power at the same problems you see progress by simply change some constants.
PS: Of course there are also software / algorithm changes, but often same problem 1,000,000,000x the processing power just works.
It sounds like @fpgaminer is saying that when humans created something similar (the neural nets of the 90's) it had issues (local maxima) until we increased the complexity (the number of variables that the system could/did respond to) in a way that started approaching the complexity of evolution.
it is impossible for complex features such as wings, eyes etc to evolve because they will require a series of mutations that do not individually confer any evolutionary advantage
The answer to this proposition is that the fact we aren't aware of the evolutionary advantages which were obtained en route doesn't mean there weren't any.
The feathered wing is very complex and it won't fly until it has fully evolved, for example -- but as we learned quite recently, feathers evolved (and were an evolutionary advantage) because dinosaurs needed to stay warm. Birds can fly because a feather which is efficient at capturing air and keeping a giant lizard warm also turns out to be very efficient at pushing air and keeping a proto-avian aloft.
> The answer to this proposition is that the fact we aren't aware of the evolutionary advantages which were obtained en route doesn't mean there weren't any.
Your argument begs the question. It is the same as saying: "since evolution actually happened, these mutations must have conferred some evolutionary advantage".
That wasn't an argument. That was pointing out a flaw in the counter-evolution argument.
The fact that we are not aware of any evolutionary advantage conferred by a change yields no information in either direction about the validity of the evolutionary theory.
It summarizes the strongest evidence for evolution in several categories, including the fossil record; the evolution of various features like feathers, eyes, and wings; sings of path dependence that can only be explained by evolution, like the recurrent laryngeal nerve[0]; etc.
It's not a single step, it's just one sign post on a long highway (you can't show all of them). Every step along the way is pretty straightforward and immediately useful.
Eyes are an interesting example, because they are seemingly incredibly complex systems, yet eyes have evolved independently dozens of times. For example, octopuses and humans have equivalently complex eyes which have entirely different origins and have slight differences (for example, human eyes have a blind spot due to the nerve fibers being on top of instead of behind the light receptors).
In 1, light from any direction will fall on all the pigment cells equally. Essentially, your camera only has a single pixel--you can't tell direction at all, only degree of brightness.
In 2, light centered on the cup will fall on all the cells, but light from the side will be occluded by the edge of the cup and only fall on one side. Now you have a low-resolution camera, and can roughly tell which direction light is coming from.
In 3, light from any angle will only light up a small part of the cup's interior, allowing for greater precision--effectively, higher resolution.
> do not individually confer any evolutionary advantage
Genes which do not confer any advantage are just as likely to spread as ones that do. Evolution doesn't select for advantages, it selects against disadvantages. Evolution is just an emergent property of death.
The point is that a mutation that causes no harm can persist, resulting in traits that serve no discernible function. Later on, multiple harmless but non-useful mutations might together make something interesting happen. Therefore the local maxima problem is not really a problem.
>Since they do not have any evolutionary advantage, they cannot spread in the population
This is not true, the question isn't whether neutral changes can spread, but simply what percentage of molecular changes that spread are neutral. In fact I think that molecular evidence has shown pretty convincingly that on the genome scale most changes are neutral, vindicating the Neutral theory of evolution:
> It says that it is impossible for complex features such as wings, eyes etc to evolve because they will require a series of mutations that do not individually confer any evolutionary advantage.
This is just false. Evolutionary theory requires no such thing and there's plenty evidence that each step towards the evolution of things like the eye provides marginal advantage to the organism even though it's not fully an eye.
Speaking of the evolution of the eye, recently I began reading the book The Vital Question (Nick Lane), and incidentally, last night I closed my reading on a discussion on that exact topic.
Allow me to quote [topic: 'The missing steps to complexity', page-45]:
"In The Origin of Species Darwin made the point that that natural selection actually predicts that intermediates should be lost. In that context, it is not terribly surprising that there are no surviving intermediates between bacteria and eukaryotes [e.g. plants, humans]. What is more surprising, though, is that the same traits do not keep on
arising, time and time again -- like eyes.
We do not see the historical steps in the evolution of eyes, but we do see an ecological spectrum. From a rudimentary light-sensitive spot on some early worm-like creature, eyes have arisen independently on scores of occasions. That is exactly what natural selection predicts. Each small step offers a small advantage in one particular environment, with
the precise advantage depending on the precise environment.
Morphologically distinct types of eye evolve in different environments, as divergent as the compound eyes of flies and mirror eyes of scallops,or as convergent as the camera eyes that are so similar in humans and octopuses. Every conceivable intermediate from pinholes to accommodating
lenses, is found in one species or another. We even see miniature eyes, replete with a 'lens' and a 'retina', in some single-celled protists [e.g. amoeba]."
One common counterargument I ever head when talking to evolutionists is that some mutations are linked to others, so a mutation can spread through the population even though it does not confer any evolutionary advantage because it genetically linked to another evolution somewhere else that indeed confer advantage.
What do you think of it? Is it serious enough? Because I think there is an obvious flaw in it, the question: why are these mutations linked?
I think you are talking about something known as hitchhiking mutations. Suppose an organism develops two mutations A and B, which lie close together in the chromosome. A is beneficial and B is neutral. When the chromosome is copied during reproduction, the copy will contain both A and B (because they are nearby). This copy will have an overall advantage because of the presence of A, and will spread in the population.
https://en.wikipedia.org/wiki/Genetic_hitchhiking
But the question remains: who put these genes near each other, so that something would evolve without being naturally selected just because its gene was near another gene?
What is the likeness of a gene near a gene that's "evolving" to be important somehow in the future of the evolution of that species?
No one did. That's not how evolution works. There is no plan, and no one decided how it would work in the future. Your second question makes me think that you're thinking of evolution as "progress", that everything is evolving towards something. It is not. That is, you're asking, given an adaption, what is the likelihood of those genes existing? But that's backwards; the genes caused the outcome.
You're trying to insert purpose or intent into what is essentially accident. Most -- almost all -- changes like these either never have lasting consequences or are eventually undone. They are insignificant, and may not even have expression, unless and until they become significant because of subsequent changes.
You can insert supernatural interference into the process -- there's nothing but the principle of parsimony (Occam's razor) preventing that -- but you can't require it in order for things to work the way they apparently do/did work.
There are many reasons. Life re-uses structures, hormones, and proteins in different areas of the body for different functions. A mutation can make a structure more efficient in one area and have little effect in another... for now, but many mutations later that mutation can become a key enabler of a whole new class of features from the secondary structure.
It may also be that the gene doesn't confer any specific advantage but a population bottleneck or isolation event can spread it nonetheless.
Writing as a practicing Catholic, I'd say that your tone sounds too peremptory, but what you're saying is right. The Church, at least, isn't in the business of second-guessing the fossil record -- and besides, there are two contradictory Creation-myths in Genesis anyways, so they must not have been meant to be taken literally. (The Church traditionally allowed and encouraged two or three different ways of understanding Biblical texts figuratively; insisting that the surface meaning is the only meaning is a Protestant thing.)
For the curious, look up _Would you baptize an extraterrestrial?_ by Guy Consolmagno SJ and Paul Mueller, which discusses this and other science-y subjects.
It's not an accident that my tone is peremptory. There is a push from certain religious groups to paint the theory of evolution as being scientifically controversial. It is not.
Evolution is a fact. There is no scientific debate about that. There are only some people who read the Bible as contradicting science, and who therefore attempt to cast doubt on science so as to defend their interpretation of the Bible.
You are correct that the Catholic Church is not one of those groups, and hasn't been for many years. The Church's official position is that God is the architect of evolution.
I'm a (protestant, FWIW) Christian and I also believe evolution. This has taken some wrestling over the years.
My current understanding is that the creation myths in Genesis are non-literal stories, intended to be taken in ancient Mesopotamian context, primarily describing that the cosmos is God's temple. (see https://en.wikipedia.org/wiki/Genesis_creation_narrative#Mes... )
My main problem at this point is that a central theme in the Bible as a whole is that death was caused by original sin, and wasn't originally part of God's creative plan. Obviously by the time mankind had evolved and sinned, death must have occurred, so I'm struggling to reconcile this one.
Agnostic of Christian cultural background here: I think part of what is meant is that murder was caused by original sin. Sure, death from other causes would already have occurred in any case, but murder is still part of our world because we evolved as K-strategists in desperate competition with other members of our species; that original sin that we are struggling to leave behind, had to be the case because such competition is what drove us to evolve intelligence in the first place.
As for creation myths, we have a document written several thousand years ago which says the universe began in a flash of light and developed through several stages of increasing complexity, which I think is pretty impressive given that it wasn't until the mid-20th-century that science established this is indeed the case.
"As for creation myths, we have a document written several thousand years ago which says the universe began in a flash of light and developed through several stages of increasing complexity"
Stages are named as days, and the "omnipotent" god even gets tired and has to rest (!) the whole day after 6 in which he makes the whole word, including the "firmament" to keep the water on the heaven from not raining down all the time.
The use of the English word 'days' is effectively a mistranslation. As for the seventh day, that's a context switch for some life advice: after work must come rest, trying to work a seven-day week is stupid and harmful - something quite a few people nowadays would do well to remember.
And God called the firmament Heaven. And there was evening and there was morning, a second day." (Genesis 1:8)
Which word of those is mistranslated?
Note that because of this and similar lines the Jews count the days for celebration (including Shabbat) to have a beginning at the evening (Shabbat starts on Friday evening).
If you mean "yō·wm" here are all the places where the word was used in the Bible:
It's the almighty that had to rest, not the people. The absurdity is obvious for everybody except the believers. But that is the definition of faith, believe, no matter what.
Easy, God has a specific meaning in mind but we are still too young to understand it.
Or the meaning got lost in translation.
Listen, if christian people (disclosure: I'm catholic) can rationalize genocide and enslavement of other people then rationalizing something like this should be easy.
But why would a single mutation immediately disappear? Isn't it possible that several generations carried on without significant advantage or disadvantage, experiencing series of mutations until the last one provided the true advantage? (I would love to know if this is completely wrong)
The usual counterargument says that just one mutation is usually enough to create a functional prototype of a complex feature/organ (MVP, if you please). A series of mutations is not required.
You're going to have to be more specific about what doesn't "sound right", because I don't see anything in that article that contradicts what you quoted.
One mutation being enough to create "a functional prototype of a complex feature/organ (MVP, if you please)"? That's not how reality works!
You can't introduce a complex organ out of the blue by flipping a single gene anymore than you can add HTTPS handling to your webapp by changing a single opcode in your binary. For that to work, the structural and operational information must have already been there in the organism.
I think that's exactly it. The groundwork for "complex" features must already be there in some sense, maybe through mutations or hitchhiking. The last mutation is probably like flipping the on-off boolean. Or maybe something dramatic like a keystone. I.e. the parts alone don't do anything, but you have this magical bit flipped that suddenly turns everything on and gives them significance.
But yeah one bit/mutation does not a feature make. Not without some prior stuff to latch on to, in my opinion.
An injection system is not an 'MVP' of a flagellum, an organ for propulsion. What doesn't sound right is the idea that single mutations often produce essentially working versions of future complex features.
If this seriously _had_ happened all on its own (apparently it didn't) then I'd be thinking the exact opposite -- this would tend to make me re-consider intelligent design.
There are plenty of objections. Polls consistently show that something like 40-50% of Americans are creationists [1]. And this doesn't mean something vague like God guided evolution, but that evolution is an outright lie promoted by scientists and possibly invented by nefarious metaphysical creatures and that in any case the Earth is only a few thousand years old, so there couldn't have been time for Evolution to happen. The fact that you probably don't know these people is more than likely a testament to how people self-segregate into like-minded groups who reinforce each others' beliefs.
All these Creationists have heard of evolution and have reasons not to believe it.
You're changing the topic. The fact that such arguments are "fully and repeatably refuted" does not dissuade people from making the arguments as much as you might think.
A (pretty smart) friend of mine tried to show me that scientists' findings about he Earth's age are wrong because he read aome article about errors in the estimation technique.
He then argued that therefore Earth is not very old and evolution didn't have time to happen.
Probably, but that's very much beside the point that a huge pile of evidence points towards theory of evolution being true.
An argument from authority (My Holy Bible says that God exists!) is quite a bit less convincing than many lines of inquiry ending up at the same place.
The usual counterargument says that just one mutation is usually enough to create a functional prototype of a complex feature/organ (MVP, if you please). A series of mutations is not required.
This study provides yet another example backing this counterargument. One single mutation can change an unicellular entity and make it behave like a multi cellular organism. Intuitively, one would think this would take many mutations. However, intuition is wrong in this case, and in many others.