Discussing the gaps in evolution theory

I've been doing quite a bit of research on evolution and biology recently, and I wanted to discuss some of the holes I see in our current understanding of evolution. Now the reason I want to take a serious look at the flaws in evolution theory is not because I want to debunk it, I'm not religious and I believe life on Earth did evolve over billions of years. The real reason is because one of my main interests as a programmer is designing systems which can simulate the process of evolution in order to generate solutions to problems without any input from the programmer. In order to design the best possible simulations I must have a very good understanding of how evolution actually works.

Lets start with some core problems. The theory of evolution implies that species will undergo gradual change over time, until eventually all those small changes amount to very large changes. This interpretation of evolution is known as gradualism. One problem with gradualism however is that fossil records show a phenomena termed "punctuated equilibrium". What this means is that fossil records show very long periods of essentially no change, and then all of a sudden a huge amount of change will happen in a very small time. In other words, long periods of equilibrium are punctuated by periods of rapid evolutionary change. One good example of this may be the Cambrian explosion.

The Cambrian explosion, or less commonly Cambrian radiation, was the relatively short evolutionary event, beginning around 542 million years ago in the Cambrian period, during which most major animal phyla appeared, as indicated by the fossil record.[1][2] Lasting for about the next 20[3][4]–25[5][6] million years, it resulted in the divergence of most modern metazoan phyla.[7] Additionally, the event was accompanied by major diversification of other organisms.[note 1] Prior to the Cambrian explosion,[note 2] most organisms were simple, composed of individual cells occasionally organized into colonies. Over the following 70 to 80 million years, the rate of diversification accelerated by an order of magnitude[note 3] and the diversity of life began to resemble that of today.[10] Many of the present phyla appeared during this period,[11][12] with the exception of Bryozoa, which made its earliest known appearance in the Lower Ordovician.[13]

The Cambrian explosion has generated extensive scientific debate. The seemingly rapid appearance of fossils in the “Primordial Strata” was noted as early as the 1840s,[14] and in 1859 Charles Darwin discussed it as one of the main objections that could be made against the theory of evolution by natural selection.[15] The long-running puzzlement about the appearance of the Cambrian fauna, seemingly abruptly, without precursor, centers on three key points: whether there really was a mass diversification of complex organisms over a relatively short period of time during the early Cambrian; what might have caused such rapid change; and what it would imply about the origin of animal life. Interpretation is difficult due to a limited supply of evidence, based mainly on an incomplete fossil record and chemical signatures remaining in Cambrian rocks.

Cambrian explosion - Wikipedia

These periods of rapid develop seem to present a problem for the gradualist. How can such a large amount of change happen so rapidly? If you've done any research on things such as genetic algorithms then you're probably familiar with the following algorithm: 1) generate a bunch of creatures with random DNA 2) test each creature to see how well they perform at the given task 3) allow the creatures to breed, with the best subjects having more children 4) apply some process which mixes the DNA together to create offspring and also apply some degree of mutations 5) go back to step 2 and test the new generation. If everything goes right, then the virtual creatures should perform better over time, as if they were evolving.

That algorithm does work, but the creatures will evolve gradually and they will virtually never experience periods of rapid change. The problem with that algorithm is that it's an exceptionally simplistic simulation of how evolution actually works. With a more realistic simulation of evolution it is possible to get much better results. For example by introducing mass extinction events and a speciation mechanism, we will begin to see signs of punctuated equilibriums. People often ask to see transitional fossils but look around at the world right now, do you see many creatures which look transitional or do they all look suited to survive in their given environment?

You could go back in time many millions of years and it would still look that way, because having half an eye ball doesn't help you see and having half a wing doesn't help you fly. That is why it's often very hard for gradualists to explain how those things can evolve. Take a bird feather for example, it's a very carefully engineered thing which gives the bird wing the aerodynamic properties required for the bird to take flight. Even the bones of the bird are structured in a hollowed out fashion to reduce the weight of the bird. This relates to a concept termed "irreducible complexity", which refers to the fact some systems are made of inseparable parts, and if just one part is taken out the whole thing stops working.

If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. ~ Charles Darwin

Many scientists dismiss the concept of irreducible complexity as pseudo-science but I think there's something we can learn by looking closely at this topic. Random mutations are rarely beneficial so we must ask how evolution is able to produce such novel solutions in times of rapid change, where is that information coming from and how does it produce complex systems which require many different interconnected parts to function? Nature clearly isn't just spitting out random solutions and hoping something works, it has a way of producing very elaborate designs very quickly when it needs to. Obviously I have some theories of my own but for now I'd like to hear what you guys think on this issue.

Cambrian explosion (or otherwise known as post-KT-apocalypse) was a period of time where there was nearly no survivor of a vast mass-extinction-event.

This left a huge hole for survival of about everything - even if it would not have been fit enough prior to the KT-event, it found a niche to survive now.

Therefore, even extreme examples of mutation had chances to survive, as there was not enough pressure from fitter competitors - those were all dead.


And "irreducible complexity" is a concept which was filed away long ago as people understood that 20.000.000 years are indeed a long time to develop something like hollow bones to enable a gliding pre-bird to overcome the problem with its weight.

Even a single bird with "better" wings would produce a progeny which could outrun every opponent in this timescale.

See, there is a major problem with palaentology: we do not find very many fossils compared to the vast amounts of time happening between those fossils.. We simply do not know about what happened to the descendants of archaeopteryx, we only took a look every 10 or 40 million years..

Darwinian evolution just doesn't pass muster. Neither does punctuated equilibrium, for the reasons you mention.

My question to you is, how did two types of prokaryotes simply appear, fully formed, on what was still a hot, inhospitable place with very little water?

Life is complex and simple at the same time.

Complexities in adaptation are the end result at any given time. The frequency and rapid advancements in any given design would have many contributing variables. Many of which we still do not fully understand. The geological record only gives clues that spurs on more speculation.

Happening slowly over time and quick spurts of rapid adaptation are both viable and from my understanding have occurred.

Life takes advantage of any given opportunity. Sometimes rapidly and sometimes slowly. Again, all based on contributing factors we're not fully aware of yet.

a reply to: ChaoticOrder

Darwin only formed the basic theory for evolution he knew there were gaps that he couldn't explain, but since then there have been many, many scientists that have searched for the answers and have successfully filed in most of those gaps. I recommend doing a bit more research on the subject with updated material to find the variables for your program.

Variables like the difference in atmosphere composition played a big role from what I remember in studies.

originally posted by: bbarkow
Darwinian evolution just doesn't pass muster. Neither does punctuated equilibrium, for the reasons you mention.

My question to you is, how did two types of prokaryotes simply appear, fully formed, on what was still a hot, inhospitable place with very little water?

And why isn't it still happening?

a reply to: ManFromEurope

Cambrian explosion (or otherwise known as post-KT-apocalypse) was a period of time where there was nearly no survivor of a vast mass-extinction-event.

Which is why I said modeling mass extinction events in simulations is important.

And "irreducible complexity" is a concept which was filed away long ago as people understood that 20.000.000 years are indeed a long time to develop something like hollow bones to enable a gliding pre-bird to overcome the problem with its weight.

Yes the evolution of wings isn't a great example, it could indeed happen gradually, even eye balls could happen gradually when you really think about it. But that's not to say I think evolution produces all systems gradually, no I think it clearly can produce complex designs with multiple parts rather quickly, and it does that using very complex methods which have themselves evolved over time. One possible explanation for the Cambrian explosion is that a so called "complexity threshold" was reached, meaning the genetic complexity of life reaches a point where evolution is able to employ a "vast range of morphological forms".

A key point I was trying to make is that evolution isn't just mixing some DNA together and hoping the offspring is better than the parents. Creating offspring isn't just a simple process of combining DNA, the mother has a complex incubation and reproductive system which will play a large role in determining how the offspring is constructed. Even during our life time our DNA can change, for example some viruses can rewrite parts of our DNA and inject their own DNA into ours. Our immune system is capable of shuffling around DNA to create totally novel antibodies and remember them in case they're needed again. Scientists have recently shown we can even pass on adaptations we've acquired in our life times.

originally posted by: bbarkow
My question to you is, how did two types of prokaryotes simply appear, fully formed, on what was still a hot, inhospitable place with very little water?

I see this as an irrelevant question. Space and/or time could be infinite for all I know, in which case it doesn't matter how improbable that event is, anything can happen with enough time and space. And how do we even know this is the only universe, or the first time a universe has been created. You simply cannot make an argument against evolution based on the probability of the first self-replicating life form occurring by chance.

Please excuse this science dunce, but couldn't man made things like Fukushima, or cosmic related events like comet impacts, introduce sudden changes to evolution?

a reply to: ChaoticOrder

As a programmer you of all people understand if one instruction is out of place a system crashes. Mutations favor decay not improvement of life forms. The odds of a program developing and writing itself are ... 0.

The answer to sudden explosions of growth after cataclysms and how life developed in the first place aren't easily answered by religious or evolution dogma.

Unless we consider life was brought here and managed.

a reply to: intrptr

Thank you. This is what I was getting at.

originally posted by: ReprobateRaccoon
Please excuse this science dunce, but couldn't man made things like Fukushima, or cosmic related events like comet impacts, introduce sudden changes to evolution?

I remember there being something like that found at Chernoble where moss was able to evolve to thrive in such a radioactive environment.

a reply to: intrptr

As a programmer you of all people understand if one instruction is out of place a system crashes.

Well yes, and that does happen in real life, some babies are born with serious problems and some don't even survive birth because their defects were so serious. However nature does have ways of fighting against bad mutations. One of the main tactics is gene duplication, some sequences are replicated thousands of times throughout the human genome. What this does, among other things, is provide redundancy, meaning if one gene gets messed up too bad then those backup copies can be used. Another thing gene duplication achieves is the ability to modify a gene and adapt it to do something different than the original gene, but without messing around with the original gene.

Wasn't this topic posted like two days ago?

Link

ChaoticOrder, thank you for writing a really well thought out and inciteful post. I have held out your very same arguments ( although not nearly as well as you have here) for years. This statement that you made really sums it up:

People often ask to see transitional fossils but look around at the world right now, do you see many creatures which look transitional or do they all look suited to survive in their given environment?

. Where are those that are transitioning? I have yet to see any species present samples of transitioning. Having said that, I do believe that each species have a great ability to adapt. a reply to: ChaoticOrder

I am always surprised that some people hold onto thetheory of evolution so tightly. Simple logic, will tell you otherwise.

[I remember there being something like that found at Chernoble where moss was able to evolve to thrive in such a radioactive environment


I think this is a great example of adaption, not evolution.

a reply to: ChaoticOrder

originally posted by: ChaoticOrder
Random mutations are rarely beneficial so we must ask how evolution is able to produce such novel solutions in times of rapid change, where is that information coming from and how does it produce complex systems which require many different interconnected parts to function? Nature clearly isn't just spitting out random solutions and hoping something works, it has a way of producing very elaborate designs very quickly when it needs to. Obviously I have some theories of my own but for now I'd like to hear what you guys think on this issue.

Well, I think the first thing to realize is that evolution doesn't actually "produce" anything. This is a common misconception. Evolution is simply the result of a process of elimination due to organisms' interactions with each other and their habitats. This idea that natural selection "produces" novel forms is absolute BS since it occurs after the novel form has already appeared. There's no way it physically manifested it in a population.

I underlined a very important point in your above statement. To me this is the question we really need to be exploring more deeply. The origin of [novel] morphological forms and novel (instinctual) behaviors is not adequately explained by random genetic mutation. No one in a million years can convince me that this is how it all came to be. There has to be a two way feedback system between genome - > environment - > genome. I get yelled at for always bringing it up, but epigenetics is the only mechanism that might be able to fill these gaps. What the research is bearing out in this field is very interesting.

And we can't dismiss behavior. Wings are useless unless the organism knows how to use them for flight and survival. The genes for this must be connected to the genes that control their development. I always wonder what comes first? The novel form or the behavior associated with how to use it. The theory of evolution (whatever it is at this point) can't explain it. It's just not equipped to.

a reply to: pointessa

Where are those that are transitioning? I have yet to see any species present samples of transitioning

The point I was making is that evolution doesn't work by gradualist transitions, it makes sudden jumps and arrives at complete solutions rather abruptly, so we never really see the transitions occur since they happen so quickly. The exact way this works is what I'm really interested in because if we can simulate that with algorithms it will be a very powerful technique for solving extremely hard problems.

a reply to: PhotonEffect

I underlined a very important point in your above statement. To me this is the question we really need to be exploring more deeply.

Well it's really an information theory question. Random mutations typically cause information to be lost, not gained, so it seems quite difficult to explain how the complexity of life can increase over many generations. It just seems to come down survival of the fittest really. In simulations, the vast majority of the population are usually pretty crap, but then there will be a few subjects who perform quite well. And in simulations it's very possible for the offspring to be worse than their parents, causing them to get worse over many generations. The main hope is that those few subjects who perform really well will have lots of kids and spread their DNA throughout the population. This is why it's so important to have modular genes in evolution simulations, simply treating the DNA as a string of 1's and 0's will produce very poor results.

And we can't dismiss behavior. Wings are useless unless the organism knows how to use them for flight and survival. The genes for this must be connected to the genes that control their development. I always wonder what comes first? The novel form or the behavior associated with how to use it. The theory of evolution (whatever it is at this point) can't explain it. It's just not equipped to.

Well I could see this happening gradually. Some gliding bird could get a bit further if it has the ability to flap its wings a little bit. It could also be like a learned thing, where it just happens to have muscles in its wings and it learns that using them can be beneficial.

originally posted by: ChaoticOrder
a reply to: intrptr

As a programmer you of all people understand if one instruction is out of place a system crashes.

Well yes, and that does happen in real life, some babies are born with serious problems and some don't even survive birth because their defects were so serious. However nature does have ways of fighting against bad mutations. One of the main tactics is gene duplication, some sequences are replicated thousands of times throughout the human genome. What this does, among other things, is provide redundancy, meaning if one gene gets messed up too bad then those backup copies can be used. Another thing gene duplication achieves is the ability to modify a gene and adapt it to do something different than the original gene, but without messing around with the original gene.

You rightly describe adaptation. Jeans aren't my strong suit. But I think I remember once that cells don't divide until the genes split perfectly, then the division happens.You don't release a program until the bugs are worked out. So if genes are that 'redundant', who (encoded) that in the programming?