Wednesday, July 23, 2008

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.

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Tuesday, July 15, 2008

Tortured Dreams

"Wake up Kalid."

I heard my name from a great distance. I tried to move, but could not. I tried to open my eyes, and succeeded - somewhat. Progress. The light was painful, but I could make out a man with a beard and an umamah. Another prisoner?

"Keef halak, Kalid," I heard. How are you? I realized I was hearing my own language again. Another prisoner, to be sure. Do I know him? He seems to know me.

"Sho...," I try to say "Who are you?" but only a raspy croak emerges from my parched throat. "Sho Ismak?"

"Insh'allah," I hear. "You survived!" The face comes into view again, closer this time. He looks familiar. Why can't I think?!

"Kalid, listen to me. You were hurt in the escape. Your neck...can you move at all?"

Escape? No, I try to shake my head, but feel nothing. "Nothing..." I try to say.

"Ok, lie still. We have to move you again, get to a safe place. Stay with me, brother!" fade again into unconsciousness.

Some uncounted time later I awake again. The light is dim, making it a little easier for me to see. I still can't move - not even my head. A rising sense of panic wells up within me, and the frustration when I cannot even flail my arms adds to the wave of fear that has taken hold of me. Am I paralyzed? Will I ever move again? What has happened to me?

I hear someone coming closer, and once again a vaguely familiar visage crosses my field of view. Brother...Ahmed! My brother? It cannot be - he is far away, fighting the infidels in Afghanistan. When I was captured he was still living out of his safe refuge in the mountain caves of Pakistan.

"Can you hear me?" he asks.


A broad smile takes over his face. "God is truly great. Yes, brother, it is I. You are safe now."

Safe? How can this be? I am trapped in this land forsaken by God, undergoing interrogation day by day. A trick! This is another trick?

"It cannot be you," I finally say. I close my eyes to slits.

I don't feel him grab my shoulders, but the room shakes around me. "Kalid - it is me. I shall explain when you feel better. Now rest."

A trick...I sleep again.

When I awake nothing has changed. Still I cannot move. Still the ceiling of the cave is the only thing I can see. I shout "Where are you!" but my voice is still muffled in my ears. Weak. I shout again. And again. Eventually I hear someone coming, but they don't come to where I can see them. "Who is there?"

"I am Abdul. Can I get you something?"

"Water, please." I feel the trickle of coolness on my lips, and I open my parched mouth to drink in what is given. "More..."

"I must go get your brother, he will want to know you are awake," I hear the man called Abdul say, and I hear him leave. Not long, I hear another approach.

"Kalid, I was told you were awake. How are you feeling?" It is the voice of the man who claims to be Ahmed.

"I cannot move. What have you done to me?" I ask.

"Brother, brother...I am so sorry. We were betrayed, and you were hurt in the attack. I am trying to get a doctor, a real doctor to come and look at you, but it is difficult."

"Betrayed? Explain."

I see the face of Ahmed again briefly as he leans over me, then settles somewhere on my side, perhaps sitting. "You were released as part of a trade. We had some of their soldiers, one of them the son of one of their lying politicians. We worked out a deal."

Then his voice bitter, he said, "But those spawn of Satan tried to trick us! As you were coming across to us, they shot you. In the back, Kalid! In the back! Cowardly dogs!" He stops, and I hear him breathing hard. "But we knew their perfidy, we were ready. Our men came out of hiding, and we managed to get you out."

A long pause. I felt the slightest of pressure on my hand. A feeling! As gladness starts to reenter my soul, I hear. "Kalid. Da'ud was killed in the escape."

Da'ud. My friend from the time of our childhood. Captured the same time as me, I saw him only once more at the prison. Even beaten and abused, his smile when he saw me managed to sustain me for weeks.

"I don't remember any of this," I said.

"What do you remember?" asks Ahmed.

"I remember being captured. I remember being tortured - the dogs, the drowning, the beatings where no one could see."

"Kalid. I am so sorry, my brother." A long pause. "Kalid?"


"I want to give you the time you need, but we must know. What did you tell them?"

Was this truly Ahmed? I was already starting to think of him so. But so many tricks... "Ahmed, when we were children, our mother...what was the last thing she told us before she died?"

"Our mother is dead?! This cannot be - I saw her only days ago! Kalid, why do you say this? What do you know?"

I relaxed. The Americans could not know this - our mother had been in hiding for almost as long as we had.

It was my brother. I was free. The horror of my captivity done.

"Ahmed." I sobbed, and once started couldn't stop. The weeks of torture, fear, loneliness came flooding over me. "Am I really free?"

Once again the slight pressure on my hand. "Yes, Kalid. You are safe. You are back with us, thanks be to God." He leans over me, and I can see him once again. "Now please, Kalid - it is important to get this in time. We must know what operations to shut down, who to move. What did they get out of you? Do not be ashamed. Many of our brothers break down, denied the chance to be martyrs. But we must know - many lives depend on it."

I sighed. "I told them next to nothing, Ahmed. Only operations long over, brothers long ago captured, cells we already know were blown."

Ahmed smiled. "That is wonderful, brother. Now let me catch you up. What do you remember about The Fist of God?"

The Fist of God. In the works for two years, it would bring a crushing blow down upon our foes.

"I remember the planning. I remember the date. I remember dreaming of the day."

"We've had to make some changes, Kalid. We've had to change the date as well. What was the last you remember?"

"The date? It is no longer to be on the anniversary of our first strike? But that was when their politicians were supposed to be in full session! Their President is only speaking there that one day."

A pause. "Somehow they got wind of the date, Kalid. We've had to find a new date. We may not be able to get their President. And we may need a new volunteer to carry out the final phase."

"What happened to Ali?"

"We think he may be compromised," said Ahmed.

"Ali? Never! I don't believe it! His cover as a page was perfect!" I remembered their conservative senator, so proper in public, so soft with his pretty boy Ali - our pretty boy Ali - in private.

"Perhaps, brother. But it has been difficult to get close to him since you were captured."

"Why? That makes no sense! It was Da'ud that he trusted most." Da'ud. My Da'ud. My dead Da'ud.

Suddenly I felt so heavy, so tired. Confused. "I think I must sleep some more Ahmed. Let us talk more on this later please."

"Of course, Kalid, of course. Rest now." I drifted off once again.

I did not see or feel the men tear the helmet off my head, pull the straps from my limbs. I did not feel or see them as they moved me to a gurney and started to wheel me out of the room, the room that no longer sounded like a cave.

But in my dreams, my endless nightmare, I hear them...

"That was a pretty close call with the Mother thing. How did you know she was still alive?"

"That was the easy part - didn't you ever listen to the tapes of his drug sessions? She was all he talked about for a while. Must have been quite a momma's boy."

A laugh. "Well, we have a lot to go on. We had nothing on that Fist operation, and now we may have enough to roll it up completely! I gotta hand it to you - I never thought that high-tech sci-fi crap would work for shit."

"Ye of little faith. Not like our boy here. Time to put away your water boarding and guard dogs, Billy. That's so medieval. And useless. You see how much more we get with a little twenty-first century tech."

"I do now. Who would have thought that those virtual reality video games had such a promising future in prisoner interrogation?"

"Me, for one. And what's even better, those Red Cross weenies can't even complain - nothing "cruel and unusual" in letting a prisoner play a little immersive video game, is there?"

Another laugh. "You're too much, man. Let's get this intel to ops pronto - and get this sand monkey back into his cage. I'm thinking it's maybe Da'ud's turn next. What do you think?"

"I'm thinking I have a new convert. Go get Da'ud, buddy - I'll run this stuff up to ops."

My nightmares...Allah, hast thou forsaken me? What have I done? Da'ud! Ahmed!

My nightmares are my reality...

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