Thursday, January 19, 2017

Not Your Grandmother's Evolution

Michael Skinner. Not Mule Skinner.
Pay attention.
I changed my mind.

I just found another bit on evolution and epigenetics from Michael Skinner in, who's getting to be my fave. My BSF. That's Best Scientist Forever.

The link is at the end.

And here're the best bits:

The unifying theme for much of modern biology is based on
Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive.

The process is also called adaptation, and traits most likely to help an individual survive are considered adaptive. As organisms change and new variants thrive, species emerge and evolve.

But this explanation for evolution turns out to be incomplete, suggesting that other molecular mechanisms also play a role in how species evolve.

Part of the explanation can be found in some concepts that Jean-Baptiste Lamarck proposed 50 years before Darwin published his work. Lamarck’s theory, long relegated to the dustbin of science, held, among other things, ‘that the environment can directly alter traits, which are then inherited by generations to come’.

Lamarck, a professor of invertebrate zoology at the National Museum of Natural History in Paris, studied many organisms including insects and worms in the late 18th and early 19th centuries. He introduced the words ‘biology’ and ‘invertebrate’ into the scientific lexicon, and wrote books on biology, invertebrates and evolution. Despite this significant academic career, Lamarck antagonised many of his contemporaries and 200 years of scientists with his blasphemous evolutionary ideas.

At the start, Lamarck might have been pilloried as a religious

heretic, but in modern times, it is the orthodoxy of science – and especially Darwin’s untouchable theory of evolution – that has caused his name to be treated as a joke. Yet by the end of his career, Darwin himself had come around; even without the benefit of molecular biology, he could see that random changes were not fast enough to support his theory in full.

(Here) is the precise definition of epigenetics: the molecular factors that regulate how DNA functions and what genes are turned on or off, independent of the DNA sequence itself. Epigenetics involves a number of molecular processes that can dramatically influence the activity of the genome without altering the sequence of DNA in the genes themselves.

Environmentally induced epigenetic transgenerational inheritance

has now been observed in plants, insects, fish, birds, rodents, pigs and humans. The epigenetic transgenerational inheritance of phenotypic trait variation and disease has been shown to occur across a span of at least 10 generations in most organisms, with the most extensive studies done in plants for hundreds of generations.

One example in plants, a heat-induced flowering trait first observed by Carl Linnaeus in the 18th century, was later found to be due to a DNA methylation modification that occurred in the initial plant, and has been maintained for 100 generations.

In worms, traits altered by changes in nutrition have been shown to

propagate over 50 generations. In mammals with longer generation times, we have found toxicant-induced abnormal traits propagated for nearly 10 generations. In most of these studies, the transgenerational traits do not degenerate but continue.

Much as Lamarck suggested, changes in the environment literally alter our biology. And even in the absence of continued exposure, the altered biology, expressed as traits or in the form of disease, is transmitted from one generation to the next.

Here's what evolutionary folks did. They used Randomness in evolution to get rid of the need for God.

Here's what religious folks did. They missed that entirely mostly and decided that the earth and the universe were only 6000 or so years old and everything happened instantaneously, more or less, spread out over six days.

Here's where we get to meet in the middle. Evolution is a thing, but
it is not a random thing. Things self-organize to solve problems of survival with intent and specificity. It's an intelligent process of reacting to the environment quickly and deliberately, not over long periods of time gradually and randomly.

It happens in ONE generation. And can persist for A HUNDRED generations.

Not gradually over long periods of time. Not randomly in any sense.

So since Randomness has gone away,

God is back.

You should go read it right now.

Now. You might be saying, what a minute! Just because Randomness is gone doesn't mean God is back! WTH!

Well. Yes, it does. If they used Randomness to get rid of the need for God, then logically if Randomness is no longer Randomness, then it's pretty reasonable to say that God is needed. That's just logic.

But. Maybe you need a bit more than that. OK.

Evolution as a theory doesn't get rid of God. Just like the good ol'
laws of nature, if the universe has a starting point, then the question, where do the laws come from, has as a possible and reasonable answer, God made the laws.

It's not the only reasonable answer, but, well, there are no other answers to the question, so you've got that or nothing.

You could then say, well, that's just God-of-the-Gaps all over again. Don't know the answer, so just blame it on God.

The problem with that is that God-of-the-Gaps is an inside-the-universe thing. Not an outside-the-universe thing.

Everything inside the universe can be explained (eventually probably) by the laws of physics.

But the laws of physics only exist inside the universe. Including, as far as we know, evolution. Which is really a process more than a law.

The universe produced the laws of physics, and evolution is
apparently derived from those, and all of that happened because of Big Bang creating the universe itself, and so we have no laws to cause Big Bang and we've no real idea at all why there are laws and particles and forces and all of that. Why there is something rather than nothing, that is.

The laws of physics are intelligent and ordered and extraordinarily calibrated to the finest of fine-tunings, and if there is only one universe (which is all we will ever ever ever have evidence for), then, well, somebody smart set it all up. Even if there are many universes, there still could be somebody smart out there in the Nothing setting it all up.

And an evolutionary process that is non-random is clearly the product of a smart somebody out there somewhere.

For lack of a better word, we'll call that God.

So here's what we're saying. If things happen in life, the universe
and everything (Nice phrase, that. I should remember it.) with clear and unmistakeable signs of an intelligence, one that empowered the universe with the laws of physics and with the amazing power of epigenetically driven evolution driving things so that intelligent observers would arrive in the universe and cause REALITY ITSELF to come into being, then, well,

that intelligence, that organizing observing intelligence outside of time and space that observed the universe into being and imbued it with organizing laws and rules so that

first there was the language of the universe (mathematics) and second there was physics and third there was physical chemistry (inside of stars) and fourth there was then chemistry (the table of elements) and fifth there was biochemistry (life itself) and sixth there were eventually observers and seventh there was Reality, then

you don't have to call it the God of Christianity or Judaism or Islam or the gods of Hinduism or the pantheonic gods of Rome or Greece,

but whatever. It's a lot like whatever God would be if God were.

And what we've already seen in previous posts is that the universe is apparently defined by 

Interactions. Relata. Relationships.

Which means that this God is likely to be an interactional,
relational God, and thus it is entirely reasonable to suggest that this God

is all about relationships.

Perhaps even and especially

with us.

Dang. That's some sweet logic.

Wednesday, January 11, 2017

Evolving Evolution

Now there's a boatload of negativity about all of this. That's because there's been so much hostility about evolution that some folks are afraid to question it at all, and other folks are afraid that it'll turn out to be true, only in a different way than everyone thinks, OR, and this is true on both sides of the argument, 

they're just not paying attention.

Both sides are stuck in arguing about Old Evolution, and they're not even aware that New Evolution is not only out of diapers, it's about ready to go to high school.

Neither side is ready for the argument to change in a dramatic, paradigm-shattered sort of way.

Curious, that.


Remarkably, the place where Lamarck was wrong was in the timing.

He thought (like Darwin) that changes in response to environment would take place over many thousands or millions of years.

Turns out, those changes can happen in one generation.


Mother to child. And hence to grandchildren. Whether or not it continues further remains to be seen. And since we don't really know what's going on yet, well, it remains to be seen.

The Old School Traditionalists are all about "Gradualism", which is that things evolve gradually over enooooormous amounts of time. Sloooowly. Tiny little random mutations that add up to big changes but it takes a looooong time.

So that's Darwin and Larmarck and Richard Dawkins (who is reputedly still alive) and all the high school and college and university textbooks. Mostly.

Then there's the slightly Newer School guys like Stephen Jay Gould (who is sadly no longer alive. I mean, sadly for his friends and family. Hard to know how he feels about it.) who had enooooormous fights with Dawkins about Gradualism, because Gould Didn't Think So.

He said that things went along pretty much as they were for looooong periods of time, and then kinda all at once, evolution happened in a much much shorter amount of time. Fast.

He called it "punctuated equilibrium", which is a fancy scientific way of saying that nothing happened for a looooong time until it was punctuated by big changes in a much much shorter amount of time.

He and Dawkins had big fights. Then Gould died. Then everybody sort of decided that the fossil record was much more about punctuated equilibrium and Gould was right after all.

Dawkins moped about and complained, but he was wrong and Gould was right.

Now, nobody had much of an explanation as to how things which were supposed to happen sloooowly didn't. Happen sloooowly, that is.

But now we kinda do. To review:

As well as being able to respond in specific ways to particular conditions, organisms seem to have evolved the ability to respond flexibly to whatever conditions they experience...

This allows systems such as the immune system, nervous system and behavioural systems (through learning) to adjust to meet whatever environment the individual faces.

And finally: ... developmental bias directs evolution ...

So NOW there's developmental bias and epigenetics and symbiosis and Complexity Theory.

Complexity Theory probably says it best. It says that using self-organization and spontaneous emergence, organisms and systems of organisms solve problems of survival with intent and specificity.

Not randomly. Not accidentally. Not always even genetically. In fact, it could be even mostly not always genetically.

Deliberately and on-purpose.

The universe organizes itself spontaneously.

That is, emergent self-organization is at the root of existence.

What emerges is not only more than, but vastly different from just the parts.

Self-organization results in higher forms of order.

But the process is unpredictable – you don’t know what you’ll get until you get it.

And problems are solved with intent and specificity.

Here's an example. It's about locusts, from in about 2006.

Scientists have finally figured out the exact moment when a jumbled swarm of creatures becomes an organized, unified, and sometimes terrifying, mass.

Examining a group of desert locusts, researchers found that at low densities, the insects were unorganized and went their separate ways. But when the group's density increased, the bugs fell into an orderly line and began to follow the same direction.

When there were a few of them together, they did not coalesce. As the group grew to 10 to 25 members, the locusts got closer to each other, but still did not move in unison.

It was only when the researchers placed about 30 locusts in the arena that the insects fell into a line and started moving in the same direction.

The march of the locusts is a bit of a mystery since they have no leader and each one can only communicate with close neighbors.

When the locusts reached a certain density, a "tipping point", then the self-organization emerged from that density. Not before. Individual locusts don't do this. It's not a genetic thing.

And what we found was something much more than just the sum of the parts, something dramatically different from the parts, almost like a super-organism, one massive locust monster from the deep.

The last sentence in the article is key. It's a bit of a mystery.

We don't know yet how it all happens.

We should probably find some more examples. What a fine idea.