Clear the Mud

An email was sent to PZ Meyers, a prominent researcher and vocal opponent of anti-evolutionists. The question subtly shocked me and yet didn't surprise me at all:

How does a tree know how to "evolve" it's seed to fly on the wind?
How would a lizard "know" that it needed to develop camouflage to
survive?

I can't imagine who any plant or animal other than human would have
the ability to "know" and as well as pass it along via DNA to future
hundreds of thousands of generations?

The super-quick answer, by the way, is: No one knows or thinks about needing to "evolve". No more than hydrogen "knows" how to condense into stars or we "know" how to grow from baby to adult.

All things follow some combination of rules: of Physics/Mathematics, of Chemistry, of Biology.

In the case of natural selection, the rules, in their most direct form, aren't that complicated once they are spelled out.


Also, the question is a fair one. But only in a world where few understand the basics of biology. There's a lot of people that share blame for this - scientist and non-scientist alike. But the fact is, it is a situation that now exists which needs to be addressed.

And - I really, really want to point this out - not knowing a thing is NOT something to feel bad about, especially when you're willing to ask questions. Yes, there's occasionally some stuck up snot who'll lord his or her pool of knowledge over you like it was a badge of honor. But that's because they are jerks.

Knowing what you don't know, and asking to find answers, is how everyone learns.

So, as I tried to do in a comment on that post... I want to try a simple summary of the concept of natural selection: Feel free to tell me if I have screwed something up here, by the way.

1. We're all random mutants:
(Which I touched on in part 1 and part 2)
Essentially every animal, plant, or whatever, is born with a number of mutations. Many, if not most, of which don't do much one way or the other. Additionally, which particular mutations each one has is basically random. One will have a mutation in this part of the DNA instructions, another will have a mutation in a different spot of the instructions, and so on.

2. Natural challenges are thrown at populations all the time:
(Which I touched on here in general and here with a specific case)
Nature constantly throws challenges at populations: Way too hot, too cold, lack of food, too many predators on the ground, a poison or toxin seeps into the environment, lake water levels shrink, water levels rise and invade areas that were once land, a massive eruption drastically alters the environment of the planet, an asteroid strikes ... really just think of something bad, and it probably already happened more than once in the world. And these are just the really drastic ones. More subtle challenges - many at any given time - happen pretty much continuously.

3. Any given challenge of nature makes some DNA mutations more beneficial than others:
If individuals have DNA changes that allow them the ability to thrive better under the conditions created by natural challenges, then they and their descendants will carry those changes forward. Those that have less ability to thrive under those conditions will be lost and take their genes with them.

4. The longer the challenge lasts, the more the beneficial changes set-in and develop:
Sometimes a severe natural challenge arises but only briefly (imagine there being a horribly bitter winter one year which really takes a toll on all the animals in an area. But then for many years afterward, the winters return to normal). In these cases, while the genetic changes - say an increase in hairiness - may have helped some survive over others, the removal of the severe pressure removes the need for that specific changed DNA.

The longer a specific challenge lasts (for example, it's not just cold for a winter, but a new ice age begins) the more this selective filtering will happen. First, the ones having the original beneficial mutation will remain the most able to survive. Then, as new mutations occur, there are new random DNA tweaks.

Again, while the new mutations are random (as they always are), it is the tweaks that continue to improve survival within this prolonged stressful environment that will endure in favor over the others - even over the tweaks that FIRST allowed them to survive. The longer this pattern continues. the more apparent the physical changes - ones that have become continuously better at their special function - will be.

5. No one knows this is happening to them:

All of this is due to constant pressure - to be more warmer, more able to hop or fly from tree-to-tree, more able to see better, run better, etc, etc. And it's all happening under all all our noses. Even we humans, with the ability to think in detail, don't know the environmental challenges that will be thrown at us tomorrow and which particular traits will help us get through them.

No one knows it's "time to change". Change happens. And sometimes a useful change happens at the right time. And so the change sets into the population. But, rest assured, no one is aware of it. What they - we - are aware of is that we are living our lives the best we can.

And that's enough of a responsibility right there. without worrying about "how to evolve". Frankly, I'm happy I don't have to worry about that.

I've got enough on my plate as it is.

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Remember the basic simplistic description I've been using so far:

• DNA is the instructions, written in a simple alphabet, that says how to build proteins.
• Proteins are the things that actually go about building you.

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But it's only wafer-thin.

How small a change in DNA is still enough to matter?

I mean, I made a big deal about individual DNA spelling errors accumulating in a population. And then I mentioned that many of them, when created, show no noticeable effect, bad or good. But at the same time I said that, with enough time and accumulation of spelling errors, sometimes there is an effect, for bad or for good.

But does that mean that a whole bunch of tiny changes have to accumulate over time, in just the right way, until the combination results in a "good" or "bad" quality?

No, it isn't necessary at all to be so intricate.

It's quite possible that a mutation is simply there, a tiny unnoticed change, in just a small number of individuals- a change that doesn't matter much. Until... an environment comes along that makes it matter.


We Want Information.
In fact, this leads into another of my new-found pet peeves regarding claims of evolution denialists.

In addition to the bald-faced lie that "all mutations are bad and/or lethal" (see part 1 and then part 2), another bizarre anti-evolution claim is that mutations do not "increase the information" of the DNA instruction book because mutations are just "random noise".

The use of the word "information" is the trick used by denialists in this case. It's a term the meaning of which denialists can keep changing in mid-argument so that they are always, magically, right. It's also something which no biologist would use in the way that the denialists do.

I tend to not worry about what they say, though. What they mean is very clear. They're claiming that mutations of any kind add nothing new to the world and, thus, can't fuel evolution.

Yes, it's kinda the opposite of when they say "all mutations are bad".

As with the "all mutations are bad" claim, this one is so wrong on it's face - so demonstrably false - that I have to conclude, once again, that those claiming it is true are, quite simply, lying.


I'll just own the word for myself, with an example.

To use their "information" term as *I* see fit, since they do the same, I will say this:

Every single mutation ever made in DNA is a bit of new information. It is a change from the previous. Whether this information is useful, harmful, or neutral, will be seen in the fullness of time. But it is something new, nonetheless, which may end up having profound effects in ways sometimes unforeseeable.

And I can think of a couple of really good examples of the smallest of changes leading to a profound effect.

Now, there's lots of general examples of mutations conferring benefits: things that make you better at getting food, using food, using new sources of food, evading predators, catching pray, surviving hot or cold climates better, and on and on.

But I think the best initial examples are ones that are almost smack-in-the-face obvious.
Ones that literally show the difference between life and death that an
incredibly small, and usually un-noticed change can make.

I'm thinking of relatively minor tweaks of the DNA instructions, which probably go unnoticed by their owners under the daily grind of life. But in the face of certain challenges thrown at them by nature, these minor differences allow the few and the lucky to survive a direct assault on their very life.

In this post, I will turn to one particular example, from the world of bacteria, the representative descendants of some of the oldest forms of life on Earth.

(In a subsequent post, I'll hit closer to home with a somewhat similar example from our own human DNA.)


Bacteria: An Instant Mob

Bacteria are, simply, single celled creatures. That is, whereas humans are made up of trillions of individual units called "cells" - all stitched together into skin, bone, nerves, lungs, the heart, etc - every bacterium is simply a single, sometimes free floating cell.

How they make more of themselves is also different from our own method. Whereas humans use sex to make more humans, a process usually involving the massive expenditure of energy, time and (for us) money, bacteria get it over with using a simpler approach.

They just grow, and when they get close to twice their starting size, each bacterium makes a copy of its DNA instruction book. It then chops itself in half, with each new half receiving a full copy of everything.

Where there was one free-floating bacterial cell, now there is two. And then it happens again: two becomes four, four becomes eight, and so on until there is a lack of food or space, which might not happen until there's already billions of bacteria.

Bacteria are rarely seen as a single cell all on it's lonesome. Since it can create its own company - one can become two in as little as hour or, even sometimes, less - it's always a population in the making.


Each one is a snowflake, er, sort of...

If we start with the simplest situation, where a bacterial population is initially just one lone cell, a population will arise simply by cells growing and dividing over and over again.

Since we started with a single cell, this population is essentially a bunch of clones of the original.

Almost.

But, remember, as with all living things, mutations -the DNA spelling errors -always happen at some rate. And as the population of cells grows in number, reaching well into the millions or billions within hours or days, mutations occur in one cell or another pretty much all the time.

So even starting from the purity of a single cell, it doesn't take very long for there to be large numbers (in the range of millions) of tiny genetic differences from bacterial cell to bacterial cell.

Now, as pointed out in part 2, the usual rules apply:

• Most mutations create no significant change in the life of any particular bacteria, either resulting in acceptable DNA spelling variations or in proteins that, though slightly different, still work the same.
• Some mutations are bad, either causing the unfortunate cell to grow slowly (pretty much a kiss of death in a population that grows and divides so fast) or by really screwing up a protein that is needed for life. In either case, these mutations rarely survive in a bacterial population.
• And then there are the few mutations that do something useful for the lucky bug.

But what is "useful" depends on the environment the population faces.


Germ Warfare

And here is where I'll pull out an extreme life-or-death example.

While there are numerous other types of benefit that are more common, they are also more subtle in effect until seen over time. My example is blatantly apparent within almost no time at all.

So, as a wee bit of extra background... a lot of people seem to think that antibiotics, chemicals that kill different bacteria, were basically created by humans. But that's not true at all.

There has been endless mortal combat between bacteria and many of the organisms on which they sometimes prey. Many antibiotic compounds arose in such beings to fight off bacterial invasion.

In fact, bacteria even fight other bacteria - if for no other reason then for simple competition over limited resources (a concept with we humans are all too familiar). Many bacterial species have developed their own antibiotics which, while harmless to their own type, will kill bacteria of other types.

One of these antibiotics which has likely been part of inter-germ warfare for a very long time, is called streptomycin. Of course, this compound has also been used by us in modern medicine.

Streptomycin stops bacterial growth. It does this by entering into a bacterial cell and shutting down all protein production.

Specifically, the drug binds directly to a critical bit of the machinery that creates all proteins in the bacterial cell, gumming up the whole works.

The result of this is the bacteria are prevented from any further growth and replication. Bacteria are killed because of streptomycin... they are essentially in freeze-frame until, over time, normal degradation begins to tear away at the cells.


Some pretty extreme Natural Pressure

So, imagine a population of bacteria is minding its own business. Then, whether due to encountering the bacterial species that produce streptomycin or due to injection of the drug by a doctor, the population is suddenly pummeled with buckets of streptomycin molecules.

At this point, the environment of these bacterial cells has changed and nature (or medicine) has offered a severe challenge to the life of the population.

Waves of the drug permeate the bacteria, binding to their protein creation machinery, ultimately leading to the equivalent of organ shutdown.

The bacteria in this population are going to die.


A hidden gift

But… as I mentioned, there’s millions of cells in this population with at least one mutation somewhere in its DNA instructions. And, again, these mutations simply arose because of an occasional accident in the copying of the DNA instruction book.

Well, one of the mutations that arose was a really simple one:

A misspelling in the DNA that tells the cell how to build a part of the protein creation machinery.

It’s just a single letter misspelling so that where the DNA had once been written with the letter “A”, it now had the letter “C”.

The result of this is the type of mutation to which I referred in part 2 as a “neutral” mutation.

Remembering the analogy from that post, where cells normally had protein-making machines with an oval chain-link at a particular position, cells with this particular mutation have machines with a square-link. (Again, this is an analogy)

Now, fortunately for these cells, this change ends up having no particular effect, bad or good, on the function of the protein-making machines. So cells with this mutation survived perfectly well, no harm, no foul - though they ultimately made up a minority of the population.

But here’s the kicker:

That tiny change, that one spelling error, that totally harmless and permitted tweak of the protein making machine actually contains a hidden gift - one that had never been noticed by the bacteria until this time.

This mutated machinery is impervious to streptomycin.

Cells containing this mutation are resistant to streptomycin attack.

So while all the other cells, with the usual machinery, are slowly being destroyed, these mutants endure. They survive. And they will continue to survive – and grow and reproduce – even in this constant cloud of antibiotic attack.

And... not only that. Their survival allowed the survival of all the other mutations any of them might be carrying. Meanwhile, the rest that died took all their mutations - good, bad, or currently indifferent - with them to the grave.

The future genetic makeup of this population has now been drastically altered - in one fell swoop.



I got your information right here

This, as one of zillions of examples, puts the lie to the bizarre claim that mutations are just noise which confer no new "information".

This one tiny change in DNA spelling conferred vast amounts of information as far as the bacteria are concerned.

They didn't realize the new message they had in their midst until they encountered the right environment. But when they did, they found that some of them indeed carried new "information".

This information - the one tiny change - conferred life, where there was, for all others, death.

And, on a broader level, it created a portal for all the genetic differences of the survivors to endure into the future.

To me, the ramifications for this population because of this one change are profound. The impact of this one genetic event, driven by a natural experience, will be detectable far into the future.

So, to claim that this is not "information" - using whatever shifting terms the denialists want - is simply willful ignorance of reality.

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The next time around (or when I get to it) I'll discuss a somewhat similar genetic tweak - with similar-ish effects - that exists in humanity. Something only recently realized with rather surprising historical roots.

Yes, it's the one people keep bringing up before I can even write about it.