Are mutations really all that random

[mishrashubham]

I've read a book named "Cheating Time : Science, Sex and Aging" by Roger Gosden. There he mentions that natural selection occurs as a process of mutations. So suppose we have some individuals of a species that have suddenly got some mutation which gives them better chance of survival in a given environment then they survive better and that's how it works.

So my question is, is it all that random? Because we usually say that when environmental conditions change the species that adapts quickly survives and the others don't. This sounds like that it is an active process that is a product of the species' efforts to survive. But Roger Gosden's description gives it a passive nature. Things occur on their own. I fit favours one well and good, the others die.

Please clear this point. thank You.

 

[NobodySpecial]

The result isn't random, the initial mutation is.

Actually the initial mutation isn't necessarily random in a mathematical sense, genes are complex and some changes are more likely than others, some changes wouldn't result in a viable organism etc. But they are random in the sense that there is no direction behind the mutation.

 

[mishrashubham]

I have the same thoughts too. Because by layman logic, the probability that the genome of a particular species undergoes mutation (which makes it survive better) precisely at the time when it is needed seems to be very very less.

Take the example of the mammoth. They evolved from primelephas, an animal that looked very much like the elephant. With the beginning of the ice age, it began developing a thicker fur of coat and to protect itself from the cold. But how did the DNA know that its getting cold and that it must change itself to include a fur coat in its bodily blueprint?

I am well aware of the usual process that I've read about in so many places, "By accident one of the animals of the species began having lots of fur. So its decendants who also had the gene for fur had a better chance of survival han those who did not. So gradually they got naturally selected."

But we must also consider practical situations which vehemently try to oppose this selection. For example most mutations are in fact harmful or neutral, so getting such a helpful mutation would be rare. Suppose that the one who develops the mutation is a male, then there is a high probability that he would not get a mate as only the top ones in the social hierarchy get to mate. Even if he does get a mate and successfully breeds, he won't pass the gene to all of his progeny. Plus there is a high chance that very few of the his offspring would survive (since survival rates of extremely young babies in the wild are very low). And what if a natural calamity occurs and kills that male or all of his offspring in one sweep? That is not a very unlikely situation. The gene which would have held key to the species survival would be lost for etrernity!

Similar problems would exist for a female as well. So according to my estimation taking into account all the above probabilities, only 4-5% of species should be able to survive through quick changes in their environment something that is similar to the ice age. Is that figure anywhere around the actual figure of how many species crossed the ice age or had decendants at least until the the ice age ended? Because if it is then I would tend to think that natural selection really is a highly random process, would come true. And random things are not supposed to be so successful.

Please answer if anyone knows the stats.

 

[Ygggdrasil]

One issue here is the assumption that distribution of species remain static after changes in the environment that necessitate adaptation. That is all species that existed before the environmental pertubation have a corresponding species after the pertubation. This is not necessarily true. For example, let's say that before the ice age, giant reptiles and mammals existed. However, mammals were greatly restricted in the environments which they could live because the giant reptiles would outcompete them for resources and prey on the mammals. However, an ice age would render many areas inaccessible to the cold-blooded reptiles. The warm-blooded mammals, whose ability to survive the cold preceded the actual coming of the ice age, would then be able to expand to these lands and fill the areas of the ecosystem vacated by the reptiles.

Similarly, in the case of mammoths/elephants one could imagine that elephants dominated most of the areas inhabitable by elephants except perhaps the coldest areas in the north where furred species of elephants could outcompete the other species of elephant. Then, when the ice age arrived, the furred elephants were able to outcompete the non-furred elephants in the majority of areas of the world and become the dominant species. This highlights another important to consider: the ecosystem itself has a wide range of "micro-environments" or niches where different species with different characteristics will live.

In both of these hypothetical examples, the ability to survive the environmental change and the associated mutations arose before the actual change to the environment. The difference is that before the change to the environment, the "new" species was restricted to very specific ecological niches whereas after the environmental change, the "new" species could expand their territory and become the dominant species. Thus, natural selection exploits the natural genetic variability and mutations that arises slowly during the periods before the environmental change. A key factor in the development of this diversity are the different ecological niches within an ecosystem that foster the development of species with differing traits (for example, colder niches, warmer niches, niches with and without certain diseases, predators, etc.) After the the environmental change new mutations will arise that will better fine tune the characteristics of the species to the new environment as well as to allow the species to try to fill new niches in the environment thereby creating more diversity of the species.

 

[mishrashubham]

Ok, so now I get it. The mutations do not arise in response to the changing environmental conditions but in fact already exist. It is only when the conditions change that the mutations come in handy to become the dominant species.

But there is also one more situation by which I am baffled. There are organisms which have developed mimicry of other organisms for their betterment. Take the example of the Fly orchid.
It is an orchid that looks like a particular fly and totally depends upon it for its pollination. What is does is act like a female of that insect by having similar appearance of a fly and also releasing the same pheromones that a female would release at the time of mating. So the male would be attracted in hopes of finding a mate but instead ends up helping the plant in pollination. This definitely happened as a product of evolution as a plant obviously doesn't have eyes to see what a fly looks like nor does it have any nervous or similar tissue to be able to think that looking like a fly would help itself.

So how did this natural selection occur. I am astounded by the fact that it copies the exact colours of the fly and also exactly mimic the chemicals of the pheromones. Let us take the usual way of describing this. A plant some fine day in a green meadow had some mutation due to which its descendants had brown flowers instead of the usual yellow or white. Now I accept that the flower won't suddenly start resembling the fly within the span of a few generations as I understand that evolution is slow process. So those who are with brown flowers are now at a disadvantage with respect to those who have yellow or white flowers (since the reason the why flowers were white in the first place was because bright colours attract insects). So gradually their population should decrease. Then they have another mutation due to which the flowers have some small projections on their sides which might look like the legs and wings of the fly. But still it does not do much to help the plant in competition. Then they have yet another mutation as result of which they get to the ability to produce and release pheromones that mimic the ones found in female flies. So now the stage is set for the males to come and pollinate the species. Thus now they are a greatly successful species having had a huge advantage over other orchids.

So this is roughly how it would have occurred. But there are two main issues with this situation as well.

1.) The only way that a male would be attracted is to have both the similar appearance and pheromones. Obviously they won't occur simultaneously and even if they did happen together, individual ones would happen gradually and slowly. So what would happen to the plant during this time? All this while the plant would be at a disadvantage as I said above. We continue the story assuming that the plant survives through every stage. However since there are so many checkpoints that it needs to cross before it is ready to take on the flies, it is highly improbable that they would survive such an ordeal.

2.) Also it very unlikely that the plant develops a pheromone that precisely fits the situation. I mean aren't the chances that the plant makes chemicals which closely resemble the ones given out by the female of an insect species that lives in the particular area where the plant grows and is also a potential pollinator, very slim? And how can it suddenly make something that matches the chemical composition so closely. Even that must have been in stages through a gradual process. Then I am not able to comprehend what would be the driving force behind the continuation of the process as at that moment there is no selective pressure on the plant to make the pheromones. Because as I have already said, this intermediary stage in evolution does not help the plant even a little bit to survive better.

But we do know that they exist today in nature. and are very successful. So there are obviously some loopholes in my thinking which I am not able to figure out. So please help. Thank You.

 

[Ygggdrasil]

1.) The only way that a male would be attracted is to have both the similar appearance and pheromones.

Is this necessarily true? It wouldn't be hard to imagine a pheromone-producing plant with the wrong colors being able to attract flies to aid in the mating. But, I agree that the changes in appearance and in pheromone production would be unlikely to occur simultaneously. It's also possible that these mutations have other benefits (e.g. the pheromone repels possible pests) or are neutral (e.g. dark colors make little difference in survival).

Unfortunately, it is very difficult to ascertain the exact trajectory by which these plants gained its traits. Some experiments, for example, testing whether brightly colored orchids that produce fly pheromone still attract flies for polination, could help suggest plausible routes for evolution, however.

2.) Also it very unlikely that the plant develops a pheromone that precisely fits the situation. I mean aren't the chances that the plant makes chemicals which closely resemble the ones given out by the female of an insect species that lives in the particular area where the plant grows and is also a potential pollinator, very slim? And how can it suddenly make something that matches the chemical composition so closely. Even that must have been in stages through a gradual process. Then I am not able to comprehend what would be the driving force behind the continuation of the process as at that moment there is no selective pressure on the plant to make the pheromones. Because as I have already said, this intermediary stage in evolution does not help the plant even a little bit to survive better.

The evolution of biosynthetic pathways is a very active area of current research, so you are asking a question that many scientists are interested in. While I don't know if there is a consensus on this issue, I'll quote the following passage from a review article that may help provide a plausible explanation for how such a pheromone mimic may have evolved:

"Secondary metabolic pathways, which are turned on in response to specific cues and make natural products, typically make a variety of products. Some pathways make only one or two products, and some make more than 100. In the language of laboratory synthesis, primary metabolic pathways are target-oriented, whereas secondary pathways are diversity-oriented. Is biosynthetic molecular promiscuity a bug or a feature? In this Commentary, we consider why natural product biosynthetic pathways may have evolved to favor molecular diversity. [...]

[One view], formulated by Firn and Jones in 1991, is based on the observation that potent biological activity is a rare property for any molecule (including natural products) to have, and that an organism needs the ability to make multiple molecules in order to hit upon the rare potent ones. Thus "evolution would favor organisms that could generate and retain chemical diversity at low cost. Organisms that make and 'screen' a large number of chemicals will have an increased likelihood of enhanced fitness simply because the greater the chemical diversity, the greater the chances of producing the rare chemical with a useful, potent biological activity." Though Firn and Jones referred to their model as the 'screening' model, it might be more appropriate to describe it as the 'diversity-based' model to emphasize the nature of the biosynthetic pathways rather than the way in which their products are used. Several features of natural product biosynthesis seem to support the diversity-based model, especially the large number of natural products with no known activity (or at least no known potent activity), the tendency of natural product pathways to produce a suite of molecules, and the widespread use of branched and matrix biosynthetic pathways to share metabolic and genetic costs."​

From Fishbach and Clardy. 2007. "One pathway, many products." Nat. Chem. Biol. 3:353. http://dx.doi.org/10.1038/nchembio0707-353 .

It is reasonable to think that a promiscuous, diversity-based biosynthetic pathway, through mutations that inactivate certain branches of the biosynthetic pathway and alter the activities of some of the enzyme involved, could produce varying amounts of fly pheromone mimic in different individuals/species and that evolution would select for those whose biosynthetic pathways are best suited for fly pheromone production.

 

[mishrashubham]

or are neutral (e.g. dark colors make little difference in survival).

But I think they do matter.

So those who are with brown flowers are now at a disadvantage with respect to those who have yellow or white flowers (since the reason the why flowers were white in the first place was because bright colours attract insects).

Please correct me if I'm wrong.

It is reasonable to think that a promiscuous, diversity-based biosynthetic pathway, through mutations that inactivate certain branches of the biosynthetic pathway and alter the activities of some of the enzyme involved, could produce varying amounts of fly pheromone mimic in different individuals/species and that evolution would select for those whose biosynthetic pathways are best suited for fly pheromone production.

I am really sorry but I couldn't clearly understand what you said. Could you please explain it again if possible? Also if you could just give a short simple language explanation of the passage that you gave (I am a school student so please bear with me).

Thanks

 

[jackmell]

It's not unreasonable to think that a healthy reproducing population with the potential to synthesize a diverse set of molecules via random mutations, could by chance and time alone, synthesize the "rare" chemical which increases their fitness, for example, a molecule which even only slightly mimics the pheromone of a pollinator and through continued selection, improve further it's molecular similarity to the actual pheromone.

I should also mention a common misunderstanding in biology that molecules have to "fit" exactly to work. That's not the case. Often, a molecule has only to "look" just a little bit like the actual substrate to work although it will usually not work as efficiently.

 

[mishrashubham]

And how can it suddenly make something that matches the chemical composition so closely. Even that must have been in stages through a gradual process. Then I am not able to comprehend what would be the driving force behind the continuation of the process as at that moment there is no selective pressure on the plant to make the pheromones. Because as I have already said, this intermediary stage in evolution does not help the plant even a little bit to survive better.

I should also mention a common misunderstanding in biology that molecules have to "fit" exactly to work. That's not the case. Often, a molecule has only to "look" just a little bit like the actual substrate to work although it will usually not work as efficiently.

Ok...so I was wrong in saying that there is no selective pressure on the plant while it is in the process of making the pheromones. It turns out that there is in fact selective pressure. Then I guess my doubt has been cleared. Thanks