The "randomness" of evolution

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(In order to ask my question, I need to explain a little bit. But I don't have a background in biology, so I may make some mistakes along the way. corrections are welcome.)

Recently I've been thinking a lot about evolution. Its really fascinating. The random exploration of the life "phase space" through mutations and settling on regions that provide the most adaptive traits for the current environment through natural selection.

But what does this "randomness" really mean? and how random is "random"?
I think when people call evolution random, they just mean that the mutations have no preferred direction, let alone a direction that gives the species more adaptive traits. But could it be that the "randomness" of evolution itself, is subject to evolution and so after some generations, the species actually evolves in a more adaptive direction?

Apparently yes. Because evolution is based on mutations and mutations are mistakes in the process of copying the DNA, you can accelerate evolution by making copying process more error prone, which can be achieved by a few patterns in the DNA(like a sequence of repeating letters).

My question is, how can evolution develop these patterns? I mean, natural selection is crucial for evolution. So if a trait is not going to make the species more adaptive in an environment, evolution can not drive that species towards that trait. these error prone patterns in the DNA are an example of such a trait. These patterns are good for the species as a whole because they make the evolution of adaptive traits more efficient, but they are not more adaptive traits for the species at an individual level and so they will not increase the probability of an individual's mating.

So how can evolution evolve these patterns without any help from natural selection?
Thanks
 
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pinball1970

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How random is random?

This link pf explores some of the questions


edit- randomness is discussed
 

jim mcnamara

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What you are talking about is called the Gaia Hypothesis first stipulated by Lynn Margulis.
Example: life transformed the environment from one without free oxygen to one with free oxygen.
Lovelock, James, (1995) "The Ages of Gaia: A Biography of Our Living Earth" is one reference.

A general overview:
https://en.wikipedia.org/wiki/Gaia_hypothesis

For the example I mentioned about oxygen:
https://en.wikipedia.org/wiki/Great_Oxidation_Event
This event changed everything on Earth from minerals in the crust to the current dominant form of aerobic respiration in living cells.

Critics of Gaia point to the fact that changes like oxygenation of the biosphere were toxic and not necessarily to the benefit of the current living organisms - in contrast to what Gaia says:
... that living organisms interact with their inorganic surroundings on Earth to form a synergistic and self-regulating, complex system that helps to maintain and perpetuate the conditions for life on the planet.
Plus you need to note that you are on the more "touchy feely" end of Biology so everyone who has a position on this thinks they understand it correctly.

Fair warning - that sentence above means: please keep this thread out of speculation. It has lots of interesting aspects.
 
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It seems I should clarify my question.
Fundamentally, evolution is the result of random mutations+natural selection. When we say mutations are random, we mean that they don't care about whether the mutation is constructive, destructive or benign to the species.

But it seems that the process of evolution itself has evolved in a way that traits that are more likely to be important in a particular environment, are more likely to be mutated.

From what I understand, a mutation is a mistake in copying the DNA. So if you want to make mutation more likely in a particular place in the DNA, you should use patterns in that area that make mistakes in copying the DNA more likely, like a sequence of repeating letters(CACACACACA...).

So basically, life not only has evolved adaptive traits for species in their environments, but it has also evolved the process of evolution itself in a way that makes constructive mutations more likely, by making sure that important areas of DNA are more likely to be mutated.

My question is that how is that possible? The evolution of an adaptive trait is possible because it immediately affects the distribution of offsprings among various groups of the same species with different phenotypes.

But the above mentioned mechanism to make constructive mutations more likely, has no such effect on the species which means natural selection won't be able to select groups with such a trait. So how is this mechanism created?
 

Drakkith

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My question is, how can evolution develop these patterns? I mean, natural selection is crucial for evolution. So if a trait is not going to make the species more adaptive in an environment, evolution can not drive that species towards that trait. these error prone patterns in the DNA are an example of such a trait. These patterns are good for the species as a whole because they make the evolution of adaptive traits more efficient, but they are not more adaptive traits for the species at an individual level and so they will not increase the probability of an individual's mating.
I'm not sure I quite understand what you're getting at. Let's look at an example, perhaps a virus. Specifically a retrovirus. Retroviruses are notorious for having especially error prone copying mechanisms. This is beneficial to the species because it enables the virus population to adapt to its host species immune system or antiviral drugs quite rapidly, as shown by viruses like HIV.

The evolution (through natural selection) of an efficient error-checking mechanism is suppressed because it would end up reducing the virus's ability to mutate as rapidly, reducing its ability to adapt to changes in its environment. So a population of viruses with such an error-checking mechanism would most likely end up being out competed by populations without one.

The only thing happening at an individual level is whether the virion (one complete virus particle) has one allele or another and how that affects its ability to survive and reproduce inside the host. The lack of error-checking machinery isn't itself an adaptive trait that helps a virion survive and reproduce, but it helps create traits that do. Hence it can be selected for by natural selection.
 
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I'm not sure I quite understand what you're getting at. Let's look at an example, perhaps a virus. Specifically a retrovirus. Retroviruses are notorious for having especially error prone copying mechanisms. This is beneficial to the species because it enables the virus population to adapt to its host species immune system or antiviral drugs quite rapidly, as shown by viruses like HIV.

The evolution (through natural selection) of an efficient error-checking mechanism is suppressed because it would end up reducing the virus's ability to mutate as rapidly, reducing its ability to adapt to changes in its environment. So a population of viruses with such an error-checking mechanism would most likely end up being out competed by populations without one.

The only thing happening at an individual level is whether the virion (one complete virus particle) has one allele or another and how that affects its ability to survive and reproduce inside the host. The lack of error-checking machinery isn't itself an adaptive trait that helps a virion survive and reproduce, but it helps create traits that do. Hence it can be selected for by natural selection.
I think this explanation falls in the trap of assuming that mutations have a goal in mind. The fact that such a trait is beneficial to the species across several generations has no effect on whether this trait is selected or not. Natural selection can only select a trait if it's beneficial to the group with that trait in the number of offsprings they have.
 

Drakkith

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I think this explanation falls in the trap of assuming that mutations have a goal in mind. The fact that such a trait is beneficial to the species across several generations has no effect on whether this trait is selected or not.
Of course it does. Population A has a mutation that reduces its ability to adapt to changes in its environment, while population B doesn't have that mutation. Over time, population B out competes population A and becomes the dominant, if not sole, population.

Natural selection can only select a trait if it's beneficial to the group with that trait in the number of offsprings they have.
Which is exactly what is happening in my example of viruses. Over time, population A has fewer offspring in total because they can't adapt to their environment as well as population B.
 

BillTre

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Recently I've been thinking a lot about evolution. Its really fascinating.
This is a complex subject which is probably why you find it interesting.
I think about it a lot as well (thus my long response).

The random exploration of the life "phase space" through mutations and settling on regions that provide the most adaptive traits for the current environment through natural selection.
This is one way many people conceive of evolutionary changes. Your phase space is often called an adaptive landscape, usually with adaptiveness increasing along the z-axis, leading adapting population to migrate "up hill". However, one should remember that the landscape would be multi-dimensional.
At the bottom of this wikipedia page is animation of the process, shown in a static and dynamic adaptive landscape. The spots in the animation represent individuals of the population which have different locations on the landscape due to their different genetic make-ups. The spots should be disappearing each generation (due to death), and being replaced by new spots in slightly different positions (the previous generation's offspring) on the population's landscape.
It should also be noted that the adaptive landscape will differ for each species (or even each individual, due to their unique composition), otherwise everything would be moving toward the same set of adaptations and other nitches would be left unoccupied.

But what does this "randomness" really mean? and how random is "random"?
I think when people call evolution random, they just mean that the mutations have no preferred direction, let alone a direction that gives the species more adaptive traits. But could it be that the "randomness" of evolution itself, is subject to evolution and so after some generations, the species actually evolves in a more adaptive direction?
So basically, life not only has evolved adaptive traits for species in their environments, but it has also evolved the process of evolution itself in a way that makes constructive mutations more likely, by making sure that important areas of DNA are more likely to be mutated.
Much of the "randomness" of evolution is attributed to the generation of mutations and the mechanisms that generate them. But as you suggest, there are cases where certain mutations can be affected by the genetic composition of the organism in question.
Genetic variation is the fuel of evolutionary change. Without variation, there would be nothing for selection to choose among. No change would happen. Mutations provide that variation, but different kinds of mutations can be limited in several ways. There are many levels at which this can happen.
These levels extend from the molecular, through the cellular, to the complex multi-cellular organisms, and even to societies that might emerge from interactions of populations.

In common (non-scientific) talk, random would just mean can't predict much what will happen ahead of time. And biological things are so complex, covering several levels of organization, each with their own set of emergent phenomena, that this is often the case. However, science likes to divid into smaller categories and examine them independently. More order can often be found there.

Here is a partial list of possible kinds of mutations.

Cause of mutations: There are many possible causes of mutations, some with the same set of effects on the sequence, some with different kinds of effects.
  • Chemical of Radiation caused sequence change: single nucleotide base changes are often considered pretty much random in what they affect. These are often used in mutagenic searches for new mutations because they are considered unbiased. DNA breaks (breakpoint mutations) rearrange chunks of DNA. This can have a more complex set of effects on genes and their activity.
  • Copying Mistakes like you mention, where there is slippage of repetitive sequences and repeated elements are either increased or decreased. These are known to underlie some disease states. Some of these mechanisms are limited to specific sequences as you point out.
  • Changes due to Biological Activity: Including changes in sequence due to things like viral insetions, activated transposons, and other "weird things". These can have a direction toward particular kinds of genomic locations due to their complex nature, involving many molecular elements some of which may have either sequence recognition of be limited to locations where the DNA is available enough for their rather large molecules to physically access particular DNA sites.
There are probably some others I am forgetting.
The point is that there are a lot of sources of genomic sequence change. These might vary independently for a variety of reasons.

Mutations vs. Phenotypes:
The relationship between particular mutations and their effects (phenotypes) is not always simple and direct.
Changes in sequence can affect molecular gene products directly in cases of transcribed RNA and translated some proteins, however some sequence changes will not effect amino acid sequences in proteins due to the redundancy of the triplet code. This means some changes will have no effect.
Effecting more complicated things like developmental systems that might require intricate controls on the development a cell. This would probably involve regulating the control of hundreds of different genes, at different times in different cells (some based on position). This could be very complex and subtle, but could still be selected for because it affects something adaptively important (reproduction, behavior, ...).
Some phenotypes (like an adult morphology) are may not be easily achievable by many genomes because they lack important genes of functional and generative systems. In genome space, they would be very far away. An example might be: If you start with an insect and mutate it (I've done this), it would be extremely unlikely you would get something with a vertebrate feature like a vertebrate CNS. It would require thousands of simultaneous changes that would be required to establish new developmental processes to generate the CNS. Within reasonable odds, each organism would have a limited set of phenotypes that it could reach. Losing functions is a lot easier than making new ones.

Other more-weird sources of mutations (changes in genome sequence) can be:
  • Hybridization: introduces a half of a genome of new stuff, could be very similar or very different in sequence, as well as copy number of particular genes, and ploidy (numbers of copies of the whole genome (normally 2 in metazoans, but can get 16 or higher). Something like 5% of the your genome, if you ancestry is from Europe, Asia, Australia, is Neanderthal. Then there's the Desenovans. Some of those transferred genes are important.
  • Some groups of fish have been shown to be the result of hybridzation, repeatedly within a group.
  • Endosymbiosis: The mitochondria had to come from somewhere (chloroplasts too). When it did, it had a big effect on the genome. Not just the addition of the mitochondrial genome, followed by it drastic reduction. Many of the bacterial genes of the mitochondrian, invaded the genome of the Archaean host cell and altered it by adding well formed functional units. But, it is also thought to have introduced a pack of molecular parasites (like transposons) that went through a period of rampant expansion, messing things up by inserting in different places in the genome, until restraining systems were evolved. This may have involved the formation of the nucleus and other eukaryotic features. Thus a set of repeated sequences were created.
    This was an important mutation (the mitochondrial endosymbiosis), but extremely rare. Life got started from inanimate matter less than 500 million years after water could form on the planet's surface (some say as rapidly as 100 million years), but it then took another 1.5 to 2 billion years for the eukaryots to evolve.
  • Lateral or Horizontal Gene Transfer: Small numbers of genes moving among populations, in bacteria and a lesser extent in eukaryotes. This is often the source of genes better adapted in a new environmental condition.
  • Genome Duplications: which have happened several times in the vertebrate lineage (and plants and insects), generate extra copies of each gene. One of the gene copies gene can then evolve completely independent functions, while leaving the older, still required functions, to the other copies.

Balancing out all of these effects on a population's genetics could result in some biasing of the mutation rate. Presumably these effects would be small in most cases. However, assuming these is a genetic basis underlying these kind of differences, it should be possible for selection to effect then, if there were consistent environmental reasons for that selection to happen.

Example (Scenario)
:
a small aquatic invertebrate dries up in a small temporary pond (this happena lot in this environment) and gets blown away. The local area (within wind blowing range) has a very diverse set of related but very different aquatic environments. You fall out of the sky into a situation different from that where you came. Your genes are not so good a match for the environment. Organismal and cellular stress results, both provide internal cell signals. This in turn might trigger a response (change in gene expression), which could include changes in the expression of genes effecting mutation rates. Such a control would make adaptive sense.

Molecular systems underlying these differences have been identified. Selection has been demonstrated. And cases of increasing or decreasing general rates of mutation have been found.
There are also well defined molecular systems for making directed and restrained mutations in specific genes, in the immune system. However, I can't think of anything like this that is inherited (inter-generational inheritance in metazoans, runs through the reproductive cells, which are a small population of cells that are not part of the immune system where these genes are being mutated)).

My question is, how can evolution develop these patterns? I mean, natural selection is crucial for evolution. So if a trait is not going to make the species more adaptive in an environment, evolution can not drive that species towards that trait. these error prone patterns in the DNA are an example of such a trait. These patterns are good for the species as a whole because they make the evolution of adaptive traits more efficient, but they are not more adaptive traits for the species at an individual level and so they will not increase the probability of an individual's mating.
There are many ways things like this can happen:
Not all sequences are under really stringent (meaning strong) selection. In the last maybe 50 years, random genetic drift has become more appreciate aas important in sequence evolution. Some sequence change will just happen with no apparent effect on viability. This means that although any gene can be mutated, not all of those mutations will have either a positive or negative effect of equal size. Some will be neutral (extreme case) and just ride along with the selection for other nearby (linked) genes in their particular that genome, which might be under strong (or weak) selection.
In addition, most eukaryotic (more complex than a bacterium) organisms will be at least diploid which can hide the effects of recessive deleterious (or advantageous) alleles in a proportion of the breeding population, due to their pairing with non-recessive non-deleterious alleles. Thus, a lot of alleles could hide, to some extent, from selection. Example: the Sickle Cell gene

There are also several levels at which biological entities can be selected for:
  • Gene selection : (selfish gene stuff)
  • Organismal (Whole Plant or Animal) Selection: that which is normally considered evolution
  • Selection among Organelles (like selection for faster reproducing mitochondria (due to their smaller more quickly copied genomes) within a cell)
  • Cell Selection with in an organism: cancer cells reproduce with a selective advantage within an organism (their environment) because they have escaped the normal controls on cell growth and movement, until their environment (the host body) dies, then they are a dead end (except for things like Tasmanian Devils and their nose cancer).
  • Group Selection: kin selection, altruism among group members
  • Selection of Taxonomic Lineages: some evolutionary lineages are very good at making more species and leave more descendant species than others. These will bush out rapidly (repeatedly) leading to more species of that taxonomic group (taxa is the general term) over longer evolutionary time periods. Those lineages that (over long periods of time) do not speciate much, could well eventually die out (some won't, due to some reason).
Species have average life spans and if they are not making new species, a species of average lifespan will die out without leaving any decedents (extinction of both the species, but possibly also the larger taxonomic lineage in which it is found). Exceptionally long lived species (like the coelacanth) can survive long periods without generating daughter species, but they are the exception. Most species that ever were, are extinct.

So, to answer your questions:
There are a lot of different ways that mutagenic rates might be controlled. In some cases, but probably not most, it is probably not dynamically regulated.
New phenotypes could be generated through either along series of simple or a few complex sets of changes. Some kinds of changes occur so infrequently that they might be considered the result of chance.
There are a lot of ways that an genetic components of an incipient trait (set of genes) may lay around the genome (involved in other processes) prior to its being recruited for some new function.
Genome duplications can provide lots of sequences that can be relatively easily adapted to new functions.
There are a lot of ways to work around these apparent barriers to evolving new traits.
 

atyy

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But what does this "randomness" really mean? and how random is "random"?
I think when people call evolution random, they just mean that the mutations have no preferred direction, let alone a direction that gives the species more adaptive traits. But could it be that the "randomness" of evolution itself, is subject to evolution and so after some generations, the species actually evolves in a more adaptive direction?
Randomness includes deterministic behaviour. Randomness is specified by the measure, and the delta measure is deterministic.

. Because evolution is based on mutations and mutations are mistakes in the process of copying the DNA, you can accelerate evolution by making copying process more error prone, which can be achieved by a few patterns in the DNA(like a sequence of repeating letters).
Mutations are not necessarily mistakes. In meiosis, chromosomes assort independently, and there are crossovers.

My question is, how can evolution develop these patterns? I mean, natural selection is crucial for evolution. So if a trait is not going to make the species more adaptive in an environment, evolution can not drive that species towards that trait. these error prone patterns in the DNA are an example of such a trait. These patterns are good for the species as a whole because they make the evolution of adaptive traits more efficient, but they are not more adaptive traits for the species at an individual level and so they will not increase the probability of an individual's mating.
Evolution is more general than natural selection. Natural selection is only one mechanism of evolution, and explains how adaptive traits (one definition of an adaptive trait is that it increases survivorship) evolve. However, there are other mechanisms of evolution that drive non-adaptive traits, eg. sexual selection. https://www.nature.com/scitable/knowledge/library/sexual-selection-13255240

Does evolution select at the level of an individual or at the level of a group or at the level of a gene? There cannot be a single answer (there are persistent debates). However, think of these things from the point of view that it is physics that is fundamental. Selection is an emergent, approximate concept, so there is no reason to expect it to be absolute.

Edit: Also, you should not mix-up the concepts of fitness (leaving offspring to the next generation) and adpativeness (survivorship). https://evolution.berkeley.edu/evolibrary/article/evo_27
 
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If you are asking how can supposedly random mutations mutate more often in a manner favorable to adapting to the being's environment, I believe it may be possible for the mutations to be more adaptive to the environment that 100% random due to an offspring inheriting some of the same/similar genetic mutation tenancies/aspects that the parent benefited from. Parents who survive due to adaptive mutations pass their genes on, so the odds of the offspring having environmentally beneficial mutations is increased, not random.
 

haruspex

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But it seems that the process of evolution itself has evolved in a way that traits that are more likely to be important in a particular environment, are more likely to be mutated.
What is your evidence is for that?
As I understand it some pathogens do seem to have evolved to be quite unstable in some genes. The advantage is rapid mutation to overcome evolving defences. Can't see that applying to more general environmental changes, though.
 

cmb

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I like the style of the OPs question and I am hoping very much if this thread could begin to expand into discussing what must be a new set of evolutionary theories that main stream science must be coming up with.

I mean, we get the basic 150 year old plot of Darwinian evolution; one individual survives better than another, and hey presto they have more kids... repeat a million times ....

But that doesn't address all the issues and I am confident that other people have augmented that basic theory with 'add-ons' and really I don't know what they are. Can biologists here tell us what those are?

Here are a couple of things I think someone in the field must have thought about and come up with answers for;-

1. In answer to the OP's point, I think one of the points that has to arrive is that, surely, the theory is actually 'survival of the generally fit' rather than the fittest. I mean, if mutation is random, as the OP proposal (which seems to make sense to me), this will give a range of characteristics, some of which may not be particularly beneficial at a given point in time. But as environments and predation changes those 'hidden' characteristics may manifest and all of a sudden within the generic mix of those individuals, those that 'had been' the fittest all of a sudden, possibly instantaneously, die out. For example, say a species living in an arid area has some of its individuals 'uselessly' born with webbed feet but it doesn't disadvantage them too much and it just happens to be a characteristic, some have more webbed feet than others. The fastest runners don't have webbed feet and so do a bit better and slowly the population are moving towards 'no webbed feet', but still it is not such a disadvantage that those individuals die out. .... and then their habitat floods ...! So I think the substance of this is not merely 'the fittest' and 'survival' but actually if a species can successfully maintain the widest set of random characteristics then it is more likely to survive. As such, this is not survival of the fittest individuals, this is survival of the species with the widest set of tolerances to environmental changes. I am sure this has been proposed by evolutionary biologists and already has a name, which would address the OPs question.

2. Trans-species jumps; if species can't interbreed (my understanding of what defines a 'species') then this means we cannot evolve 'from' another extant species that then carries on its own evolutionary path. What it means is that we can have long-gone ancestors in common with current day species, but one species evolving from another and then continuing to co-exist is excluded. I think that is fairly obvious but it is not excluded from Darwin's original proposition as far as I can tell. I'd have thought there would be some theoretical expansion of this point, and if anyone can say what the current thinking/theories are that would be good.

3. Rate of change of species; A common ancestor of ours to other primates (as far as I know) is the Miocene Proconsul (https://www2.palomar.edu/anthro/earlyprimates/early_2.htm) which is said to have lived from 21 to 14 million years ago. But if it took 7 million years to become a new species then why is that an unrepresentative timescale for the 14 million years since then? I mean, surely there are more than two evolutionary 'species' steps from proconsul ape to us? Maybe not? I don't know? What do updated evolutionary theories say about this? I mean, taking that thought further, if we look at the first 'modern humans' 250,000 years ago, if one was here today they could integrate into society, we'd be able to have offspring with them and (presumably with training!) talk together. Yet that is 'only' 1/40th or so between proconsul ape and us, and it looks to me like there are going to be more than 40 times the number of differences between early homo sapiens and proconsul ape? Again are there any modern theories to explain what would initially appear to be, presumably, sudden accelerations in changes of species?

4. Given the total number of species on the planet, and that evolution occurs by seeing new species coming into existence, what does statistics of the past say about the rate of bifurcation of one species into two species, and are we seeing that rate of bifurcation today? I mean, just for primates alone, there appear to be a few hundred known species (https://en.wikipedia.org/wiki/List_of_primates) so is there some statistical inference when we should see the next bifurcation of a primate species, and when was the last? Is there a theory which quantifies this?
 

cmb

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What you are talking about is called the Gaia Hypothesis first stipulated by Lynn Margulis.
Example: life transformed the environment from one without free oxygen to one with free oxygen.
Lovelock, James, (1995) "The Ages of Gaia: A Biography of Our Living Earth" is one reference.

A general overview:
https://en.wikipedia.org/wiki/Gaia_hypothesis

For the example I mentioned about oxygen:
https://en.wikipedia.org/wiki/Great_Oxidation_Event
This event changed everything on Earth from minerals in the crust to the current dominant form of aerobic respiration in living cells.

Critics of Gaia point to the fact that changes like oxygenation of the biosphere were toxic and not necessarily to the benefit of the current living organisms - in contrast to what Gaia says:


Plus you need to note that you are on the more "touchy feely" end of Biology so everyone who has a position on this thinks they understand it correctly.

Fair warning - that sentence above means: please keep this thread out of speculation. It has lots of interesting aspects.
Something I came across just recently is the proposal that, actually, one of the dominant sources of oxygen at certain times in Earth's history was not biological in nature but radiological. I had assumed it would 'only' have been biological, but I can see that is in error now. What the proportion of bio- to radio-logical is, I guess is for future research?

 

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