Clear the Mud

The intro to this attempt at being a smarty-pants who knows less than he thinks is here.
Please read that first, so you can get the context of where I'm coming from.
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To recap:

• Everyone was born with mutations.
• Most of these mutations have little or no effect on your ability to live and flourish.

But, on occasion, a mutation makes a difference.

“Oh my GOD! It's a MUTANT!!!” ... well, no, it's probably something pretty un-amazing...

Deformations are the most obvious mutations to us.

Although, even then, many things that are technically “deformations” are nothing more than the minor variations that we all have when compared to others.

But some, of course, are serious – ones we usually call birth defects generally cause problems which decrease the likelihood of surviving to adulthood. Of this type, most are so severe that such a one would likely never even make it through pre-birth development and would not even be born.

These are the ones - aside from the ability to shoot ice from our hands or to look like Hugh Jackman - that people commonly think of as “mutations”.

But the rest... are a little more subtle.

Sometimes, a mutation makes a difference right when it emerges - if it affects something immediately important in how something physically develops or it's ability to continue living.

Other times, even though it changes something physically (whether you can see it or not), a mutation may not impact anything enough to effect an organism's development or life *if* it doesn't really impact the needs it has in that particular environment.


Relative benefit, relative harm

So, as for mutations that do have a noticeable effect.

Some cause harm, possibly minimal, possibly huge.

Some cause a benefit, possibly minimal, possibly huge.

AS an example, we can consider changes that affect an organism's ability to obtain or efficiently utilize food.

Some possible beneficial results of a mutation that increase the ability to obtain energy from food:

• Can outrun others to get food,
• Can forage better or root around for untapped food sources,
• Can eat items not commonly eaten or too harmful for most to eat,
• Can use strength as a tool to either kill animals easier or fight off competitors
• Can biologically extract more energy from less food (net result, you need less food to survive)

Some possible detrimental results of a mutation that decrease the ability to obtain energy from food:

• Slower, when speed is important for getting to the food
• Less ability to forage for food sources (anteater with a stumpy snout?)
• Less ability to tolerate food types, especially when those are the only foodstuffs available.
• Less physical strength when ability to take down an animal is critical or when competition for food is carried out by strength.
• Able to extract less energy from the same amount of food (net result, you need more food to survive).

(As a side-comment: notice that being "the strongest" is just one of many things that may - or may not - help an individual to survive. Some people, even today, insist on interpreting a famous term "Survival of the fittest" to mean some form of "Survival of the strongest". This is absolutely wrong.)

Now it’s important to note here - with this food acquisition example - that in times of plenty, there might be so much food available that everyone has enough to eat and there’s no particular harm or benefit to the above changes in ability, assuming they are not too severe.

In this case, where the pressure caused by food availability is very low, it's possible to have a population of animals with both the original food-using ability and the altered one to be intermingled without any noticeable advantage of one over the other. If the environment is not one in which this mutation is noticed, there is little pressure on the animals with the relatively decreased ability.

It’s when food becomes more scarce that any benefit or harm, food-wise, will become noticeable to the population.


Just able to make it through

Under this pressure of nature (ie, sudden limited food sources) the harm or benefit of any abilities will ultimately be noticed in one way:

Which ones are able to survive this pressure, and which ones are not.

Compared to those better equipped to cope with the pressure, more of those individuals that are less able to survive the pressure will succumb before they have children. And so the genetics that caused them to be less able to cope will diminish in the population over time.

Taken to the extreme, if the pressure (ie, lack of food) continues long enough, over enough generations, the genes which resulted in a lesser ability to cope could ultimately be gone from the population.

But note: all the survivors had was simply a better ability to deal with a particular circumstance over time. It could have been lack of food, it could have been too cold or too hot, or increased radiation, or a new disease, or anything else you can think of.

Usually it's many of these at once.

Nothing about an individual's survival, or more importantly, the genetics behind it, says anything about it's superiority or advanced nature.

That which allowed survival was simply the best thing available at the time.


Not more advanced, just the fortunate recipients of survival

To drive the point home, there have been uncountable numbers of species that - after all their "advancement" - suddenly ended up without even a "best". Given a particular challenge - some lasting numerous generations, others happening abruptly - most species on Earth, after millions of years getting through all sorts of things, one day found themselves with nothing that ultimately could save them.

So, in the end, the use of the term "good genetics" (a term I've heard tossed about) is something I find particularly annoying. That term is so vague that it is essentially meaningless. But the way people use it is to mean something like, "to be more advanced".

This is simply false.

On a purely biological level (as opposed to philosophical), the fact that we, each of us, is here on Earth means nothing more than that we (via all our ancestors) made it through the hoops and hurdles of time.

More likely than not, in many cases, we just made it.

We are all a mish-mash of thousands of things that were good enough for government work. Some functioned well, some even exceedingly well, and some just got us by. Some things got tweaked to work better, others still truck along almost the same as they were when they first appeared.

Nothing about us is, in any way, perfect. And biologically speaking, we are not in any way a goal of this process.

Biologically speaking, we are each, simply, an amazingly fascinating, walking, talking collage of things that worked.

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In the next post, I think I'll discuss a more extreme type of challenge to populations. Something more life-or-death extreme.

The intro to this attempt at being a smarty-pants who knows less than he thinks is here.
Please read that first, so you can get the context of where I'm coming from.
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Quiet Accumulations

To recap from the first post: You, and everyone you know is a mutant.

And remember the basic description:

• 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.

Most mutations neither harm nor help:

If we all start with a couple of hundred mutations in our DNA, why don’t we all have three arms and twenty eyes - or at least look like Hugh Jackman?

I suppose it's worth making a semantic distinction here. In saying "mutation" and "mutant", I am referring to spelling changes in your DNA instructions (the mutation) and the protein or organism which is encoded by the altered DNA (the mutant). And that is typically exactly what is meant by those words.

However, most of us think of a "mutant" as the end result - some person with a demonstrable change from the norms of humanity - a six-toed foot, for example. Using that more common usage, then probably not everyone is a physical mutant. Although, changes from the norm are often not in things visible to the eye, so you never know.

So, here’s the deal: most genetic mutations have no major effect on how you function as a human or how you look, at least compared to the normal variations seen throughout humanity.

In these cases - again the most common - the net result is that there is no discernible difference between how you function with that mutation and how you would function without it. It is a fact of statistics and the way DNA and proteins work that most mutations will not actually cause any real problem or benefit at all.

It's the same difference:
In many cases, this “no harm, no foul” result is because the particular mutation in the DNA instruction causes absolutely no change in how the proteins – the actual machinery and materials of you - are built. This is called a “silent” mutation.

There’s a detailed reason that this is possible - but for now, just think of how you, a reader of English, would interpret the words “color” and “colour”. Depending on where you live (the US or UK), one is probably the preferred spelling, but you know that they both mean the exact same thing – it’s just a minor spelling variation about which most English speakers are forgiving.

Essentially the same thing happens with many words in DNA instructions. There are quite a number of DNA words that can be spelled with minor variation and yet mean precisely the same thing.

So mutations in DNA that simply result in accepted spelling variations will not change the protein that it encodes in any way at all.

Close enough for government work:
Other times, the change is not a simple spelling variation but actually does alter how the protein is built. However, even with a change in the structure, many changes are minimal enough to actually keep the protein functioning in approximately the same way as the original. This is termed a “neutral” mutation.

Imagine you had instructions to make a chain to lock a bike to a bike rack. The instructions call for 50 metal oval links and a very intricate lock mechanism on one end.

And the instructions are not in the shorthand we might be used to, like this:

Link 50 metal ovals together, add lock on the end.

The instructions are more linear, step-by-step, no matter how repetitive it seems, like this:

Start - add metal oval - add metal oval - add metal oval - add metal oval - (this is repeated 46 more times)

Followed by the (likely) hundreds of individual steps to make a lock from scratch, attached to the chain of links, and then it's done.

Now, imagine the instructions got slightly garbled so it suddenly said to do this:

Start - add metal oval - add metal oval - add metal SQUARE - add metal oval - (this is repeated 46 more times)

Well, a metal square link isn't quite the same as a metal oval link, but it still serves the purpose of being a solid link, and the chain is about the same length – so, in the end, we still have a perfectly usable bike lock system.

These "neutral" mutations happen quite often. And, in these cases, it’s almost as harmless a change as the previous type of silent mutation.

( Note: A very different outcome might have happened had we mucked about with the very intricate makeup of the lock mechanism, or if a metal link had been replaced with a link made of silly putty.)


Sooner or later... the day comes when you can't hide from what you've done anymore. A day of reckoning.

As mentioned previously, at conception, every human child is a recipient of a couple of hundred of these type of mutations. Now, considering your DNA instruction set is made up of a few billion letters, this is an almost imperceptible amount of change.

And because silent and neutral mutations, introduced one by one in the DNA instruction book, are often not even noticed, this allows genetic mutations creep into a population over time.

But over time, over many generations, it begins to add up. Think about this:

You inherited a few hundred mutations from your parents.
You give all of those plus a couple hundred more to each child you might have.
They give yours and your parents’ mutations to their children.
And those children (your grandkids), in turn, give the mutations from your parents, you, your child, and themselves to your great grandchildren.

And it goes on.

And this has always been happening since before we were born and will continue to happen long after we’re gone.

And those are just the simple spelling errors. There's far more dramatic mutations out there as well.

Because of all this, the changes accumulate.

And, again, many of these end up being no benefit and no harm.

But at some point, for one of many reasons, a mutation - be it a brand new one or a combination of older ones - will make a difference.

For one of your descendants, who knows how many generations away, this accumulation of mutations could ultimately lead to something very harmful.

Or, almost as likely, they could result in something that will save their life and the lives of *their* descendants.

Or it just might make their eyes bluer.

You really won’t know until the day that it kicks in.

But that day (or many days, or century, or millennium) ends up being very important.

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Working topics for subsequent posts (Just so I have it down in print. And so people can say, "hey you never wrote that one!"):

• We are the things that worked
• The tiny difference between life and death
• The confusion of language: "The theory"
• The confusion of language: "The fittest"
• There's always something new
• You think living is easy? (The Second Law of overlooking the obvious)
• ...?
  

Note: the intro to what it is I think I am doing is here.
Please read that first, so you can get the context of where I'm coming from.


1. You are a mutant.

Yup. You're a mutant.

This is in response to the following claim that is often made:

All mutations are bad. They cause horrific birth defects. There is no way a mutant can survive, nor can anything good come of mutations.

It's usually a claim made to "prove" evolution is false.

Of course, this one is so factually wrong that it's kind of a joke.

In fact, it's so astonishingly wrong, that it can really only be called a lie.

Why?


Because, you are a mutant.

I know I already said that, but I'm just reinforcing the point.

You are a mutant and you can not deny it. Well, not if your honest.

And by the way, I don’t mean that half of your DNA came from mom and the other half from dad and so, therefore, you are different from them. That’s true, too. But I don’t mean that.

Keep reading...


I mean that you are, from the very beginning of your genetic existence, the result of mutations.


Here’s a bit of what I mean - just a little bit. For starters, if your Dad compared the DNA – the instructions of life - that were in any of his sperm cells (please be adults here) and compared it with the DNA that he was first given at conception he would find, as you might expect, that they are a nearly perfect match.

Nearly.

But not quite.

What he would find is compared with the DNA he had at the beginning of his life, the DNA in any sperm cell contain a couple of hundred simple mutations. This is a consistently demonstrable fact, a consequence of the slight imperfection of the machinery that copies our DNA.

So, his sperm contain numerous mutations.

And his sperm, with those mutations, along with your mother's egg, also with some mutations, made you.

So - without question – you are a mutant.

And to be clear, me too.

And pretty much every other living thing on Earth.


How so?


Your instructions were copied less-than-perfectly

To think about this, let me just describe some background with a way too simple and utterly inaccurate analogy:

Your DNA is a book of instructions, written in a simple alphabet (as it is made of only 4 letters, unlike our 26 letter alphabet).

Now, this instruction book is sometimes described as a "blueprint" of your body. However, that’s a bit inaccurate.

All your book really contains is the diagrams to make a wide variety of tools and materials that are, generically, called “proteins”.

And it’s these proteins, each one described in your DNA instruction book, that work together in an amazing dance of combinations and permutations to build you and every other organism on Earth.

So, again:

• 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.

OK... given that background, what is a mutation?

The most basic description of a mutation is: any change somewhere in the DNA instructions.

There are many types of changes that can happen, some massive and some almost imperceptible, but I’ll focus on the simpler ones.

Imagine someone has your book of DNA instructions and is given the task of making a copy of the whole thing by hand. (And in fact, this copying happens all the time in most of the cells in your body.)

OK, so, the guy who’s doing the copying is pretty darn good. He rarely makes mistakes and he’s also very diligent at double checking his work so as to correct the occasional error he does make.

So the copy is really, really pretty darn faithful to the original.

But… it’s a big book. Once in a very, very long while, the copying guy misspells a word (In the analogy, say, “cat” is copied as “car” or “kat”) and also happens to not notice the error, so it doesn’t get corrected.

Once he’s moved on to later pages of the book, there is no going back. The error is now a permanent part of the copied book.

That’s a mutation.

Other times, he might accidentally delete or add one or many letters. (In the analogy, “color” becomes “collor” or “colour”)

These are also mutations.

There are even more elaborate ways that changes in DNA instructions happen, but these basic ones illustrate the point, I think.

And these things happen often enough that by the time a dad’s sperm and a mom’s egg are created, and then they meet to ultimately lead to a new life, there’s already a hundred or so mutations locked in to the baby-to-be.

Every baby starts off with around 100 simple mutations.

Every baby is a mutant.

You are a mutant.

And yet most of us are not particularly unusual compared with anyone else, to the best of our knowledge.

Why?

(I originally ended with "Why?" to mean I would go into more detail in the next post. Alternatively, though, you can feel free to offer up thoughts on that very question.)
---

Working topics for subsequent posts (Just so I have it down in print. And so people can say, "hey you never wrote that one!"):

• Quiet accumulations
• We are the things that worked
• The tiny difference between life and death
• The confusion of language: "The theory"
• The confusion of language: "The fittest"
• There's always something new
• You think living is easy? (The Second Law of overlooking the obvious)
• ...?
  

I am still trying to feel out how best to do this thing here. But here's an intro to where I'm coming from.

My frequency posting here will likely start out low.

Whether it stays low or not is a separate issue...

Anyways... the introduction.
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I used to love it, then I didn't:
It's only been recently that I've regained enough of an interest in the sciences to really comment on them.

It's amusing to me and at least one of my old grad school friends that, after almost three years away from the sciences, this should happen.

See, while in the midst of in-the-weeds benchwork, there were periods where I was so bummed about some technical problem or other, that I often avoided all science reading outside of my little world. It just made me sad for reasons I won't go into right now.

So I would learn all about things very specific to my work but which would mean almost nothing to anyone walking in off the street.

And then, for many and varied reasons, I left the sciences, resulting in me having a PhD mainly for decorative purposes.

What woke me up a bit - people with megaphones and no truth:
So, for a while, when science-type or medical-type issues came up, I generally held my tongue or, more often, just walked on by.

But I'm learning one thing about myself. I don't sit well when there are issues that I happen to understand a bit and yet others, who by their words know very little if anything, use a public stage to spout off misinformation or out-and-out lies.

Now, as in politics, people using these tactics in anti-science or anti-medicine crusades are usually doing it for a reason. This group is sometimes countered by an opposing group which attempts to promote discussion to demonstrate why the first group might be slightly off-base in their claims. But they, themselves, are not likely to change their tune no matter how much reasonable discourse is offered. Their minds are made up and all things that exist in the world do so in order to prove that person's worldview is absolutely correct.

Little can be done in those cases. That's usually not so bad, because the number of such people is relatively small. Unless, of course, they have a megaphone.

That's when the real danger begins. It's the third, and by far the largest, group of folks - the ones who don't know the details of the argument - who are in danger of being turned toward believing the ones with the loudest voice. This becomes especially likely if those attempting to propagandize are armed with single bits of selective information or carefully chosen quote snippets, sometimes from "authorities", sometimes from the person or group they are attempting to demonize.

And, look, I'm aware we all do things like that, differing mainly in degree of duplicity and target of our attack. Some people will almost over-cautiously couch their rhetoric to remain truthful, fair, and allow for a benefit-of-the-doubt - practically negating the argument. Some will fire away but then retract the more glaring errors of their words. Others will feel no concern for such niceties and will let the bile fly far and wide, without regard to accuracy or hypocrisy.

I suppose it's the last group that concerns me the most. Certainly when it comes to the topic of science and medicine.


The Big "E":
Not surprisingly, this has come up in the context of biological evolution of species, being an absolute fact of nature, the mechanisms of which are still under reasonable scientific debate.

I remember what got me started noticing this - sort of lifting the fog from my brain in regards to attacks on reality.

As I was poking around the web one day, I stumbled on a post or something which proudly claimed they had the proof - PROOF! - that evolution was false.

Wow. OK, this could revolutionize science. How exciting. What was it?

It's called the Second Law of Thermodynamics.

Um... really?

I remember reading this and just... scratching my head.

See, it'd been a while since I cracked open a physics book but, among other things, these concepts of thermodynamics have been around for a while. You'd think if it somehow managed to concretely disprove evolution, someone might have brought it up - and more importantly, proved it.

And, upon reading the explanation, I began to see that the person explaining this "undeniable proof" didn't understand much about biological life or, I suspected, physics. Others have gone in-depth to destroy this particular argument, but I'm happy to discuss the basic argument and the simple reason it doesn't make any sense as a post at some point soon.

Anyway, ok, thermodynamics is kinda over the head of me and most other folks, so I could just let it pass.


However, as I kept poking around, I saw more and more things that truly disturbed me.

Selective quoting, fact-mining (picking just the one bit that makes it sound like you're right), or complete lies.

• Evolution claims we came from mud! (it doesn't)
• Evolution claims whites (or whomever) are "superior"! (it very much doesn't)
• Charles Darwin claimed in his own book that natural selection couldn't work! (Really?!?)
• An astronomer said evolution is false! (He also said the Universe is not expanding. Wrong on both counts. Right about the formation of atoms in stars, though!)
• There is no fossil evidence that evolution occurred! (except for the thousands of fossils)
• Evolution doesn't explain gravity (True. It also doesn't explain why Nixon was such a creep, Ben Stein, so that's two points from Evolution, I figure.).
  
• There are NO CROCK-A-DUCKS!!! (WTF? Oh my God!)
  

... and on and on and on---- and ON AND ON AND ON.

Oh, and it's amazing how many directions they come from, pulling random bits from every corner of the intellectual realms - places no one else would even have dreamed of (ie, thermodynamics). And yet, each one simply ends up proving the point that the basics of evolution have held up for a century and a half for a reason.


The one that was one too many:
But there was one that just finally and completely pissed me off when I read it.

It pissed me off royally because anyone who knew ANYTHING about the science he is criticizing would know this is false.

The claim is this:

Natural selection, if it were real, would depend on mutations occurring in animals, plants, etc.
Any change in DNA is bad.
Mutations are bad.
They make mutant babies.
Most die at birth. The rest rarely mate.
So mutations can't drive evolution.
Therefore, evolution is false.

Wow.

Look, people, if you don't know even the most basic facts of a topic, you shouldn't be criticizing it.

This applies to politics, personal life, electrical work, and for the love of all things, people, the ultimate fact-based thing: science!

Of course, when has that ever stopped anyone from mouthing off before. Yeah, I've done it, too.

But anyway, it was this basic lie - that mutations are all bad and/or lethal - that sort of did it for me. It is such a breathtakingly wrong statement, so demonstrably false, that no one with even basic biology training could actually come up with it.

And if they didn't have that training or, better yet, didn't bother to look it up from an authoritative source - because everyone needs a refresher - then why on Earth would they say such a wrong thing and not expect to be called on it?

All that made me decide to start from this point - the question of mutations - and work sideways.

I figure I could do my teeny-tiny little part and at least address some of these deceptions, one-by-one, in my own fashion and for whatever small bit of good it might serve.


So I started with the simple fact that each and every one of us is, in fact, a mutant.

... and then we'll see where it goes from there.