The New Larmarckism

One of the most remarkable developments in biology in years is the discovery of epigenetics. A more technical discussion is down below, but let me start with an analogy.

DNA has often been described using a recipe metaphor. The recipe is just some words on a piece of paper, but describes how to combine ingredients in the environment to produce a dish.

A chocolate cake is quite different in looks and taste to the ingredients that go into it. And we all know that the quality of the ingredients, as well as the skill of the cook combining them, can dramatically influence how that cake turns out. Even though the recipe is exactly the same.

It's the expression of the recipe that makes the difference between good cake and OHMYGODITSDELICIOUS! cake.

This last idea is Epigenetics. That is isn't just our DNA (recipe) that determines how we will develop. How that DNA is read and expressed has just as much to do with the outcome as the basic recipe does.

Which means that what you eat, drink, smoke, huff, shoot, and accidentally expose yourself to can affect not just your body for that hour, day, or week, but how your cells will develop from then on. And more importantly, it can affect how your kids will develop as well, long after the exposure.

(For you Intelligent Design advocates out there, if you think the recipe analogy makes the case for an Intelligent Chef being necessary for the meal, I'm afraid you are once again confusing scintillating metaphor for scientific method. They are not the same. One is a useful method for predicting outcomes, the other is just words that tell a story. Sound familiar?)

More Technically...

[Wikipedia] ...the term epigenetics refers to changes in gene expression that are stable between cell divisions, and sometimes between generations, but do not involve changes in the underlying DNA sequence of the organism.[1] The idea is that environmental factors can cause an organism's genes to behave (or "express themselves") differently, even though the genes themselves don't change.

This is huge.

Your environment (which includes what you eat and breathe, as well as what you *do*, like exercise, read, think) can cause a change in gene expression. This concept has been around a couple decades, and is being exploited in all kinds of genetic therapy ideas (viral, miRNA, siRNA).

What's new and interesting is that these changes can be permanent. They can stick around through cell replication, so all new cells of that type now behave differently in the same way. This is epigenetics.

And what's truly new and remarkable is that it has been shown that these permanent markers that change gene expression can also modify germ cells (sperm, and probably eggs) in the same way. Meaning that what happens to you in your environment can not only change you, it can change the genetic legacy you pass on to your children!

Early indications are that many forms of cancer, schizophrenia (and other mental health failures), obesity may be caused not only from your environment, but could have been caused by experiences of your parents or grandparents.[link - requires subscription]

For example, if Mom smoked before getting pregnant, but quit and never smoked again once she had you, your genetic expression will still be different than if she had never smoked at all.

This is just the teeny, weeny beginning of a whole new understanding of how evolution and genetic expression works. Soon we will not only be able to cure our own genetic disorders, we can make these fixes permanent and inheritable. A further understanding will allow actual improvements to your existing genetic recipe. And these can be passed along to the next generation as well.

Have you ever thought, "If I could change anything about myself, what would it be?"

Start making your wish list.

Mind Games

We have so many misperceptions of the world. Contributing to this are "blind spots" in the way our bodies and brains have evolved.

Here is a list of some fun sites that explore various sensory "blind spots."

(You can't trust your eyes)
Your brain will make stuff up
And it may ignore what's actually there
Things can change right in front of you and you won't notice
You can miss huge gorillas
http://www.psych.ubc.ca/~rensink/flicker/index.html
And lots of other interesting misperceptions of color, contrast, and shade

(you can't trust your ears)
http://www.exploratorium.edu/exhibits/highest_note/ex.about.fr.html
http://www.kyushu-id.ac.jp/~ynhome/ENG/Demo/illusions2nd.html

How our expectations affect what we hear:
www.mrc-cbu.cam.ac.uk/~mattd/sine-wave-speech

Vision/Sound systems affecting each other:
www.faculty.ucr.edu/~rosenblu/lab-index.html (Look for McGurk effect under Demonstrations)
www.cns.atr.jp/~kmtn/soundInducedIllusoryFlash2/index.html

How thoughts and emotions can affect how you perceive things:
https://implicit.harvard.edu/implicit

So...How do you feel about witness testimony in your trial?

Crazy Monkeys

In David Sloan Wilson's book Evolution for Everyone, he tells a story about crazy monkeys, and the evolutionist explanation for why this behavior, though seemingly contra-survival, can keep coming up in a rhesus monkey population.

Here are the basics (paraphrasing the book). Every generation, a small faction of males in a rhesus monkey colony active as if they are out of control. They take insane risks in jumping between branches. They bully and rebel, can't be controlled by their mothers or by their peers.

The first theory the researcher, Dr Stephen Suomi, was that perhaps this behavior conferred an advantage to the psycho males - they could enter a new group, take over with their bullying and crazy behavior, mate with the females whether they liked it or not, and thereby perpetuate their genes.

But experiments showed that this theory was wrong. Rejected by family and friends, the psycho males never learn to compete well with other males or to fit into a group. Rejected, they typically lead a miserable solitary existence until they die. So why doesn't this sort of maladaptive behavior die out?

The answer appears to be that the same gene that causes males to go crazy turns out to produce confident, capable females who achieve high status within their groups. These females breed more, and, just as important, due to their enhanced abilities are even able to raise sons with the "crazy gene" to be fine young monkeys. Mothers lacking the gene who gave birth to sons having the gene (thanks, Dad) weren't so effective, and the crazy gene expressed itself to produce crazy monkeys.

So the gene stays active in the population, and due to the statistical dynamics, about 10% of male rhesus monkeys get the crazy gene, with a smaller percentage of these not having the advantage of corresponding super mom who end up acting...crazy.

The basic story of the crazy monkey - adaptations that thrive work for the group (or species), not necessarily for an individual. Certainly, at an individual level they can't be too destructive or they would die out in a population. But they don't have to be individually helpful, and can sometimes be individually hurtful.

For the longest time I've wondered about religion, and how some of the craziest acts of humans seem to come from religious extremists.

Initially, I used simplistic explanations. In searching for better answers, I looked to neurobiology. Antonio Damasio has produced some great work on how emotions work (and are in fact necessary) in reasoning. Better yet was Pascal Boyer's Religion Explained, which went into some evolutionary origins concepts for religion, and did pretty good job of explaining what religion was (and wasn't), and how our brains dealt with it.

But this only got into the proximate reasons for religious tendencies (meaning that it helped explained why people act religious, but not why these brain structures and cultural structures developed in the first place). For the trait to become so widespread in our species, it must have some larger effect that helps species survival. (In evolutionist terms, proximate causes are the immediate biological or physical mechanisms that cause a behavior or outcome. Ultimate causes are the species level reasons why such a behavior or outcome propagates through the generations more effectively than others).

In Darwin's Cathedral, David Sloan Wilson gets into these proximate and ultimate causes of religion. In his theory, the ultimate cause of religion is that it is adaptive at a group level. In other words, religion is a mechanism that causes people to group together with common purpose. (Clearly there's more to it than that - otherwise he couldn't fill a whole book. But the gist is that religious tendency in the human brain is a proximate cause which supports an ultimate cause of forming groups that perform better than individuals, or even of other groups that aren't so cohesively knit).

Getting together into cooperating groups doesn't require religion. And certainly having religious feelings and irrational beliefs don't always result in forming a cohesive group. But individuals who initially developed the genetic variation producing the god module portions of the brain had powerful feelings, and connecting with other individuals with similar feelings (to the exclusion of those who didn't) made sense. And because these feelings evoke such powerful emotions, this mechanism provides a very strong social glue for like individuals. Groups who can collectively whip themselves into a religious fervor can feel more connected, and more cohesive, than those who group based on less emotional drivers.

This is finally a reason which makes sense to me, and which is consistent with known facts of religion. This is a group-supporting behavior, like altruistic punishment, that provides survival and propagation benefit to members of the group over members outside of it.

Personally, I may not like the fact that the mechanisms of religiosity periodically result in a crazy monkey. But I can understand the selection advantage to groups with strong binds and common purpose, which religion historically has provided.

Colonial Expansion

To understand how intelligence can emerge from groups of simple cells, it helps to have examples of other emergent behaviors.

Hive animals, such as ant and bees, work in ways similar to the ways in which cells in our body work, but because they are "bigger", they're easier to study.

Let's look at how bees manage to figure out the best place to go get nectar every day.

Bees look for nectar that they then take back to the hive to make into honey. The higher the sugar content of the nectar, the more efficient the bees are at making the honey. Bees are pretty good at finding the best sources of nectar, even when those sources change. How is this done? Is there some guiding intelligence that takes the reports back from the worker bees and decides to send all the other workers to the best spots?

In a sense there is a guiding intelligence, but it is an emergent intelligence, based upon statistics and feedback loops in a system. Here's how it works for bees. The worker bees head out in random directions looking for nectar. When a bee finds nectar, it collects some then comes back to the hive. It then does a little "dance", which other worker bees at the hive can watch to learn the directions to the nectar.

Different bee species have variations on the dance, but basically the orientation of the dance correlates to the relative position of the sun or the direction of the nectar relative to the hive, and the length of the "waggle" portion of the dance is correlated to the distance from the hive. The worker bees in the audience can head out in the correct direction and the approximate distance, then look for the nectar source.

Ok, neat, this is how other bees can find nectar more efficiently than just every bee randomly searching each time. But when you have lots of different nectar sources, how do most of the bees go to the best nectar source? If they're all coming back and dancing about random nectar locations, then the audience bees should also be spread out among the random sites.

But...the time spent on the dance is driven by the richness of the nectar. The bee gets a buzz on, and the better the buzz, the longer he can dance. With bees coming and going all day, those bees that dance longer will have a larger audience of bees - more bees will catch their act if they perform it ten times rather than just once. So all those bees go find the better buzz, and they too come back and perform longer dances, which grows exponentially to send even more bees to the better source.

Each bee just follows a few simple rules. Step one - get ready to leave the hive. If you see a bee dance while leaving the hive, stop and watch it, then orient yourself in the right direction and fly ten waggles thataway. If you don't see a recital going on, just leave in a random direction. Remember to count how many waggles you fly, and in what direction relative to the hive (or sun).

Now look for nectar. If you find some, take it back to the hive. Pass the nectar to another type of bee, then go perform. Perform as long as you feel the energy to perform.

Go back to step one.

If you model this, you see that no matter where the best source of nectar is in a given day, most the bees will end up heading for it, thus optimizing the nectar collection for the hive.

No single bee made a decision. Nobody passed along the information to the (nonexistent) decision makers. The dance says nothing (directly) about how good the nectar is. Nor is there any "debate" among the bees about the relative merits of the different nectar locations. It was purely the inherent mechanism that the better the nectar, the longer the bee could dance, and the statistics inherent in that fact that drove the "intelligent" behavior of the hive.

"That is real intelligence," you say. Well, it's a smart move on the part of the bees, certainly, but it isn't how humans make decisions. (Or is it? I'll come back to how groups of humans make decisions in a later post).

What this example highlights is how separate "cells", each just doing what comes naturally, can create a higher order "emergent" behavior when the cells are in a group. Studies of human organs indicate similar sorts of statistical emergent behaviors in blood cells, liver cells, and even brain cells, where the normal biological functions of the cells and the chemical byproducts of these functions create a form of communication between cells. Groups of cells (an organ) also work with other organs for even higher order emergent behaviors. Our organs use chemical signaling (such as nitric oxide, hormones and neurotransmitters) and electrical signaling (such as potassium and sodium ion channels).

Understand that all of these mechanisms develop over time through the evolution of genetics. Those mutations that provide better survival and breeding in a given environment become standard in the later generations. Bees that could dance longer given good nectar statistically attracted more bees to the right place, so the hive outperformed other hives that didn't have workers with this trait. Over time, only those hives who had workers with this trait were the only ones around.

Evolutionary theory isn't just for biology, although it's pretty amazingly useful to help understand how and why organisms are the way they are. This powerful concept can be applied at any level of organization - including brain organization, and even human social organizations. The exact same principals apply.

I'll try to put together examples of each of these in the following weeks.

Moral Relativity

Whether or not something is "good" depends entirely upon the level of organization and the environment in which is exists.

You, as a normal human being, are a social organism made up of a lot of other living entities. Large groups of cells, whether organized into tissue or organs, or living in colonies like bacteria, "cooperate" to form your body. In the same way, each cell depends upon even smaller (although still complex) structures, such as mitochondria, ribosomes, membranes, and many others. (In fact, a mitochondrion is really itself a separate organism, living inside your cells...but this story is for another day).

If a cell is "misbehaving" (such as in a cancer or other harmful mutation), what's best for the organ (and organism - you) is to kill the cell. From the cell's perspective, this option really sucks.

But why would a cell risk being killed? Lots of reasons. A lot of what the cell does as a whole is driven by the "cooperative" behavior of all those cellular structures we talked about - mitochondria, DNA, RNA, membranes, and such. If something changes in the behavior of one of these members, then the overall behavior of the cell may also change. And the immediate rewards may encourage such behavior, such as unchecked replication and growth.

But as with most dynamic systems, the surrounding community of cells (or some specialized cells) may take action against the non-conformist cell, perhaps bringing it into line, perhaps just killing it. (Sometimes the cell itself will commit suicide!) Thus a tendency toward the status quo, an inherent conservatism built into a stable organization.

At each level of organization, it isn't immediately obvious to the individual components what "good" behavior is. And good is, obviously, relative. It really depends upon the level of organization, the environment, and the "goals" that determines "goodness" (where I define goodness as furthering the progress of the organizational level toward set goal).

Without defining the organizational level, goal, and environment any concept of "good" or "bad" ascribed to behavior is meaningless. It just is. The cell changed - it now made copies of itself unchecked. Good for the cell. But probably bad for the larger organism/organization in which the cell lived. So the cell was killed. Good for the larger organization. Bad for the cell - no matter what its goal was, it's sure not going to achieve it now. (Unless the goal was death - in which case, Way To Go, Cell!)

The parallels to social theory are obvious, and have been used quite a bit in the last century. The good of the individual human being vs the good of the group has been ripe ground for applications of theories in social structure. The group can be a family unit, a neighborhood, a community, city, a state, even a species.

Benefits can accrue to individuals who attempt to cooperate in a larger group. The level of group "allegiance" can vary quite a bit from individual to individual, and game (and evolutionary) theory has a lot of fun trying to work out the relative cost/benefit equations for these trade-offs.

And humans are well adapted to this sort of group cooperative behaviors. Evolutionary theory would say that's obvious. If working as a group confers advantage to individuals in the group over individuals who are not in a group, then over time individuals who work well in a group will proliferate more than those who don't.

Rogue "cells," such as a terrorist, can produce significant local change. With the technologies being made available, this change can reach quite a bit further than local. Think nuclear, or worse, biological weapons. The cells may think they are doing the right thing. They might not see themselves as cancers - perhaps they think they're mighty immune cells! Their mission is to wipe out the foreign viruses that threaten to change the very DNA of the stable host society!

I'm not the first to wonder about the social parallels. In fact, it was the following quote that made me start thinking about this. What has changed is that it is only recently has science started to get to the point where is was possible to actually do something about it.

I am prepared to assert that there is not a single mental faculty ascribed to Man that is good in the absolute sense. If any particular faculty is usually good, this is solely because our terrestrial environment is so lacking in variety that its usual form makes that faculty usually good. But change the environment, go to really different conditions, and possession of that faculty may be harmful. And "bad," by implication is the brain organization that produces it. - W. Ross Ashby, 1962

I see the battleground of today is being defined as western concepts of progress and individual liberty against the backlash conservatism of religious fundamentalism (typically anti-science, anti-"progress"). I hear questions like: Is globalism and consumerism and what's best for the individual what is also best for the planet? Or do we need to revert to the "good old days," of strong hierarchical (typically religion based) control?

I think we're asking the wrong questions. We need to think of new models of social organization. Ones that provide the best chances for species survival, that better check the rogue individual (be they terrorists, CEOs, or Presidents). But that do so in a way that enables the creativity and progress that comes from free thinking individuals.

It's likely that these new models will require that we take our own brain evolution in hand and modify it as required.

Most of what we think of as "moral judgments" are made as a result of genetic hardcoding produced by evolution. In Moral Minds by Harvard's Marc Hauser, reports of experiments and studies show that moral decisions are made "intuitively," with various rationalizations for the decision produced after the decision is already made.

Interestingly, and perhaps counterintuitive, there don't appear to be any real differences in fundamental moral choices in people of different cultures, or people of different religions. In fact, even people with a religion and those without make the same choices, suggesting that inbuilt morality is independent of learned religious frameworks. We don't think our way through moral decisions - we just react.

So where does this leave us? Our moral decisions are made based upon our selected genetic wiring. That wiring was selected for being "good" for the majority of breeding individuals, given the environment (including social structures) that existed prior to now.

If the environment changes, be that the physical or social environment, those decisions may no longer work. They're no longer "good," regardless of what worked before, and regardless of religious dogmas. And as we see, "good" also depends upon whether we're talking about the individual, the country, the species, or the planet.

Like the example of the cancerous cell, individuals who threaten the planet threaten all species of life that we know of. These threats can be immediate, such as terrorists with WMDs, or more subtle, such as governments who do nothing about resource depletion, global warming, and other "let the next generation deal with it" type of threats.

What could we adjust that make us less likely to follow the crazy leaders, more likely to look at long term consequences?

Ignorance is Blessed

The U.S. is about to hit escape velocity on the crazy bus.

From the most recent MSNBC/Newsweek poll...

13. Do you think the scientific theory of evolution is well-supported by evidence and widely accepted within the scientific community?

Nearly half (48 percent) of the U.S. public said no; one-third (34 percent) of college graduates say they accept the Biblical account of creation as fact.

These are the same people who go on to make educational videos like this one which "disproves" evolution.

It's times like this I start rooting for the antibiotic resistant staff bacteria to colonize the Discovery Institute...

Public Sex

Why is public sex illegal?

A friend asked me this recently (don't ask why - let's just say it came up). Anyway...we decided to verify our assumption that having sex in public was, in fact, illegal. A quick web search determined that aside from a number of state laws that proscribe what kind of sex one can have, and with who, it turns out most of the laws against public sex revolve around anything that "offends public decency."

For the most part, it appears that if you perform any act resembling sex (even fully clothed, acting like you're having sex) and someone sees it and takes offense, you can be prosecuted.

So back to the question - why?? I mean, if you really think about it from an evolutionary perspective, it seems so counterintuitive that this would be proscribed. But (in the U.S. at least) we've all grown up with this strong taboo and we don't think twice about why. (Well, okay, maybe some think twice or more about it - clearly my friend and I have. But you still don't see much of it. Or if you do, you live in a more interesting neighborhood than I do).

Here's the evolutionary argument.

I think you'll agree it's a given that most people like sex. (Those that don't tend not to pass this trait on to the next generation, so it tends to die out).

In fact, some surveys indicate that most people think about sex multiple times a day. Every day. Again, given the obvious evolutionary argument here, this shouldn't be much of a surprise either. (Great recent recap of the research here).

So...most people like sex, think about sex every day, and would like to have sex a fair portion of their waking minutes (and many of their sleeping ones as well).

So given that this appears to be one of the most common, natural impulses of humans everywhere, why don't we support having sex in public?

The obvious answers, of course, is that we're all prudes in the U.S.; that people love to make laws telling other people how to behave; and any laws that require only that one person be offended for an act to be a crime would tend to squelch excessively exuberant behavior.

But being interested in behavioral evolution, I wanted to investigate more. Evolutionary theory would say that unless there were a breeding disadvantage to a behavior, over time it should die out. Prohibitions against sex are definitely a disadvantage to breeding.

More research led me down a number of garden paths with little satisfaction. Some related to classic (and overused) arguments regarding males need to ensure paternity (selfish genes), female fertility cycles and receptivity, monogamous relationships, protection of children, "we are not animals" (yeah, right).

All of it left me cold, because in every case the big large pink and blue elephants in the room were ignored, such as the eternal proliferation of prostitution and the enormous economics of the sex industry in general, both of which provide direct evidence that there always is huge pent up demand for sex that finds an outlet somehow. (Though I did learn a new word in the search, which is always cool.)

So again - how did these prohibitions against public sex evolve in so many cultures? (Side note - not all cultures have this prohibition. For example, people used to (and still do) live in small houses, or even huts where everybody is in one room. Sex is carried within sight of everyone else in the household. It's apparently ignored, treated as just "one of those things", like taking a piss). But this isn't common).

One argument my friend and I came up with involved the productivity hit to a society - that if everyone was having sex anytime they felt like it, nothing would get done. One could envision a societal evolution model of two cultures competing for resources, where one redirects sexual energy toward behaviors that better benefit the group as a whole and therefore outperforms the other culture that is still laying around humping in the street.

Another idea is maybe those caught by the enemy tribe (or lions, tigers, and bears) with their "pants down" were killed and weeded out, and only those who had sex in "safe" places survived to reproduce. But probably not - when exposed to danger, your best bet for survival is to be surrounded by friendlies, not off by yourself. If exposure to danger was a large factor, we would more likely have a taboo against having sex without other people around.

After batting around a few other ideas, we finally just gave up and had fun envisioning a culture where public sex was legal and acceptable. The porn industry and sex trade dies out - you can get better for free on any street corner. Sanitary Engineer takes on a whole new meaning, and stock in cleaning products skyrockets. Breastfeeding is no longer the primary concern of the religious right. Cluster fucks are no longer a bad thing. "Would you like to be seated in fucking, or non-fucking?" Everyone is reminded once again that there is good naked, and there is bad naked. (Hmmm...maybe that's the answer...)

Try to come up with a few yourself - it's pretty fucking hilarious (if you'll excuse the pun).