Evolution

11 Mar’15 ~QofDay~ Evolution Information

Mutation explains how existing genetic information is changed, but it doesn’t explain where new genetic information comes from.
So the question is “How does evolution add information?”

Hi Bhatta,

Have you ever done the “chinese whispers” thing – where a circle of people whispers a message to the person next door – and you start with a message and see what come out after it has gone round the circle.

One classic was a message passed during battle from a front line commander to the commanding general – it started out as “send reinforcements, we are going to advance” and by the time it got to headquarters it was “send 3 and 4 pence we are going to a dance”.

Mutation can occur in many different ways:

Addition,

Deletion,

Mistake in copying,

Duplication,

Inversion

And many other levels of variations on these basic themes.

One of the most powerful mechanisms is duplication followed by drift.

Some areas of chromosomes, particularly those associated with immune response, have various mechanism that encourage very rapid mutation within specific areas of the genome, in response to particular environmental cues.

It is an extremely complex area of study, and one that can take hundreds of hours to get a decent feel for.

Mutation provides the source variation.

The selection pressure of selective survival turns that variation (essentially random noise) into information (something with a use), in a very real sense.

[followed by]

Hi OM

To get into the details of the many possible mechanisms that cause mutation is a major exercise in chemistry and physics. I’m not sure how far down that rabbit hole anyone really wants to go. Everything down there is in terms of probability functions – nothing “hard” at all in terms of knowledge.

And the actual mechanics of some of the processes, in terms of the shapes and behaviours of some of the molecular systems involved are sublimely beautiful. And there is a lot involved, momentum, complex shapes, complex electric and magnetic resonance at the molecular and atomic levels.

At the other end of the spectrum so to speak, to get into the subtleties of the holographic effects of selection operating on all influences of every gene simultaneously.

[followed by]

Hi Bhatta,

At the simplest level, two classes of outcomes give bigger molecules – addition and duplication.

There are many different sorts of mechanisms at the atomic and molecular level that can lead to either sort of outcome.

There are classes of molecules that attend DNA and repair breaks that sometimes happen.

Sometimes those repair molecules add in extra bits that weren’t there previously. Typically additions of that type are small, but they can be of any size, with probability reducing with increase in size.

This sort of error is rare, but even if it only happens one in 1,000,000 repairs, and repairs happen about once a day, then in a large population, that results in quite a bit of variation.

Duplication of entire chromosomes usually results from a failure of some aspect of the spindle apparatus that lines up and divides the chromosomes equally during division (particularly during mieosis, the process that halves the number of chromosomes during gamete production). These sorts of mutations are usually lethal, but every so often (about 1%) manage to survive and breed.

And there are many different mechanisms at the molecular level that can give these results. We have identified quite a few, and I have no reason to think we have gotten even close to 50% of the possible mechanisms yet. I suspect there may be a huge class of possible mechanisms that occur with very low probabilities. We seem to have identified most of the higher probability mechanisms.

It is just really difficult for most people to get their minds around the sorts of numeric complexities that are involved in the molecular activity within cells. It is vast – beyond any possibility of any human mind ever understanding the whole range of possible activity even within a single cell, let alone a colony of cells with as many cells as the cell has molecules.

We can understand the main processes, like having a map of the major highways of a country, but not have any idea of the paths actually walked by every single individual within that country, every day of their lives. Actually that problem is millions of times smaller than understanding a cell.

[followed by]

Hi FOS

The evidence for the change from fish to bird is there, in the fossil record, and in the genetics of the individual descendants alive today.

And it is often hard for people to get that everything alive today has been evolving for an equal time, from the simplest of bacteria, to the most complex of life forms (possibly us). So in a very real sense, the forms that are present today, even if they look exactly like forms in the geological record, may not be identical to those forms at the molecular level – evolution has had a long time to change the chemistry even if the outer form remains the same.

One thing to get about evolution is that it selects for survival in particular environments.

Some forms are very well tuned to survival in particular environments, and remain stable in those environments, but that doesn’t mean that all aspects of the chemistry remain identical.

When explorers arrived in New Zealand they saw a shell fish they recognised, and called it a cockle. It looks exactly like the cockles of England, and lives in exactly the same sort of habitat. But it comes from a completely different family of molluscs. It is an example of convergent evolution, where a particular form is so well suited to a particular environment that evolution ends up taking many different routes to the same form. There are many other examples, that just happens to be one that I am very familiar with.

Evolution tunes populations to the specific environments in which they live. The smaller the population, the faster the tuning process. This is one of the reasons that we see small jumps in the fossil record. Fossils are most likely to form as a result of large catastrophes. The few animals that survive those catastrophes tend to be in small isolated populations, in very different environments to the ones that had existed prior to the catastrophe, and so often there is major change in those small populations in quite short periods after the catastrophe and there is a very low probability of any of those individuals being fossilised and an even smaller probability of any human being actually finding one of those fossils.

And in terms of going from fish to bird, we have thousands of intermediary forms (but not millions). So at a certain scale, we can see a smooth transition, but if you look closely you see gaps in the smoothness, just as one would expect from the general scenario in the paragraph above.

When one looks at the molecular evidence, within the DNA of living descendants, then the story is quite different.

Here we see evidence of usually (but not always) gradual accumulated change over time.

This is easiest to see in the structure of some of the highly conserved molecules.

There are some processes, like the conversion of electrons into phosphorylated adenosine, that are essential to metabolism of all oxygen using life forms. Some of these molecules (like cytochrome C) have structures (shapes) that are so critical that even small changes are usually lethal, and so they are generally conserved (change is very infrequent). So the very few changes that do actually occur and survive give us a very strong indication of relatedness between species. Looking at hundreds of such molecules within thousands of species, we are able to build very strong probabilities around the sorts of molecular evolutionary paths that have probably occurred over evolutionary time.

It is a fascinating study, if you have the sort of mind that likes visualising the shapes of molecules and visualising multidimensional probability distributions (which I do). I spent a couple of years at university studying this stuff, and have kept an interest over the last 40 years, reading some of the abstracts of journals most weeks, and occasionally delving into the details of the papers. So I am definitely not a professional expert, and I am a very interested amateur.

As Richard Dawkins clearly describes in his book “Climbing Mount Improbable”, evolution often has to take very strange routes in getting from any place in possibility space to any other place, because every step along the path has to be of benefit, or at least not of significant cost. A population may be able to compete against another population for a significant period if it has some mutations that carry some small costs, but those mutations end up going to some configuration that gives a large advantage. But if the costs are too high for too long, then that population will be out competed by other populations not carrying such costs.

So there is a little room for evolution to explore into areas of selective disadvantage, but not too deeply nor for too long. Most such mutations lead to extinction, but not all.

Being able to visualise the multidimensional probabilities of such things is something I find profoundly beautiful, and it is not something I can easily share with anyone else, just too complex.

The evidence is there, and for the most part it is deep in the chemistry and deep in probability, in the structure of DNA and a knowledge of probability theory. Not too many people willing to put the hours into either to get a real appreciation of them.

[followed by]

Hi OM

Everything other than the “bacteria” in the deep ocean requires oxygen.

Only organisms that have evolved the haplo-diploid (sexual reproduction) life cycle have evolved any real levels of multicellular complexity – and only the oxygen users have managed that.

And there are “bacteria” (including whole phyla of Archea, fundamentally different from other bacteria) down there, and deep within fissures in the rocks, that can take energy from electrons that are from chemical sources, not sunlight. Most come from the electrons available from hydrogen sulphide, and there are many other variations on themes that use other molecules. Very few are common now, because the sun capturing oxygen producers have created an atmosphere of oxygen that is toxic to all such life forms, and they can only now survive in very specialist environments, where once (a billion or so years ago) they had the entire ocean and the entire surface of the planet (prior to plants creating free oxygen).

And from one perspective, one can view human beings as movable anaerobic environments supporting bacterial colonies far more numerous than our own cells (within our gut). So evolution is rarely clear cut in its distinctions of what is controlling what. Things often influence each other in many different ways. It is really very, very complex.

About Ted Howard NZ

Seems like I might be a cancer survivor. Thinking about the systemic incentives within the world we find ourselves in, and how we might adjust them to provide an environment that supports everyone (no exceptions) - see www.tedhowardnz.com/money
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