The Amazing what?

We need an appropriate noun in there…I just wish “atheist” wasn’t one of them. After his awful run-in with Martin Hughes in which TJ Kirk, the “amazing” atheist, revealed just how mind-bogglingly and obliviously racist he is, you can guess what happened next.

A. He had an epiphany and realized that lecturing a black man on the nature of racism was absurd?

B. He took the rebuke seriously and is in the process of rethinking his errors?

C. He doubled down and declared that black people in America are all professional victims?

What’s your guess?

The correct answer is C, D, E, F, G, H, etc., in increasing order of patent nastiness. Kirk had a long heartfelt discussion with Hughes, and it just got worse and worse and worse.

This is exactly why we have to dig a deep chasm in the heart of atheism, detonate a few nukes inside it to widen it, and fill it with molten lava to keep those shitbags on their side.

But of course @DeepakChopra is incorporating epigenetics into his quackery

quantum_chopra

I guess I shouldn’t be surprised that my prediction that epigenetics was ripe for an invasion of quacks would come true. I also shouldn’t be surprised that Deepak Chopra has already jumped on the bandwagon.

We are referring to a different aspect of our genome, which radically revises a model that is decades old, dating back as far as the original discovery of DNA. In the original model, the effects of our genes were considered to be fixed and unchanging, controlling every aspect of our physical makeup, behavior, and susceptibility to disease. Not just eye color, height, and other physical characteristics were predetermined by inherited genes, but perhaps all kinds of behaviors, from criminality to belief in God.

No. No one with any knowledge of biology seriously believed any of that. Look up norms of reaction, for example — phenotype is the complex output of interactions between genes and environment. What he’s describing is the popular misconception of how genetics works.

It does not fill one with confidence when Chopra’s opening gambit is to completely misrepresent the field of science he’s claiming to be revolutionizing.

The new model, however, portrays a more fluid, dynamic genome that responds quickly, even instantly, to all that we experience, including how you think, feel, speak, and act. Every day brings new evidence that the mind-body connection reaches right down to the activities of our genes. How this activity changes in response to our life experiences is referred to as “epigenetics.” Regardless of the nature of the genes we inherit from our parents, dynamic change at this level allows us almost unlimited influence on our fate.

Yes, action affects gene expression. If you exercise, for instance, your muscle fibers will upregulate cytoskeletal proteins, repair enzymes, etc. in response. How else does he think we get changes in physiology?

This is not epigenetics, however. It is also not heritable — your muscle cells do not contribute to the plasm of your progeny.

Theories of evolution and genetics have long taught that genetic mutation is entirely random. However, genetics has been gradually stepping into a new era of “self-directed biological transformation,” a mouthful perhaps, but with great significance in each word:

  • Self-Directed: Voluntary activity in your thoughts, feelings, habits, and desires. This is the realm of personal choice

  • Biological: Effects at every level of the mind-body system, including reactions by your genetic material

  • Transformation: Major shifts in cellular activity leading to physiological changes

Repeat after me: we do not have conscious control over our histones or DNA methylation. We do not have conscious control over our histones or DNA methylation. We do not have conscious control over our histones or DNA methylation.

You cannot think your gene regulation into a desired state. What is most ironic is that someone who doesn’t even understand gene activity wants to put it under his control. Imagine self-directed aeronautical transformation: every passenger in a 747 is given direct access to every little detail of the actuators and hydraulics and circuitry of the plane. Would this be good or useful? Would transformation into a greasy flaming crater be desirable?

It’s also wrong. Voluntary control of your thoughts does not translate into voluntary, directed control of your genes.

This means that control is being given back to each person; we are no longer seen as puppets of our DNA. The human genome is set to be the stage for future evolution that we ourselves direct, making choice an integral part of genetics. This is in stark contrast to the “biology as destiny” view where genes override choice. Unless decisions, lifestyle, environment, and personal preferences are included, a full picture of the mysteries of our DNA cannot be attained.

I get it. Chopra is peddling an unrealistic illusion of control over your body, that you can modify your physiology by thinking at it. Nothing he is proposing is at all revolutionary — when you go to the doctor, and they tell you to “eat less, exercise more”, they are telling you that you can redirect your overall pattern of gene expression in productive ways. They’re just not swaddling it in uselessly vague misappropriation of scientific concepts.

Have you ever gone to a doctor who tells you your destiny is totally fixed by your DNA, go ahead and smoke, drink, engage in risky sexual behaviors, eat deep-fat-fried Mars bars, etc., etc., etc. because none of it makes any difference to your health, since your fate is fixed by your DNA? Didn’t think so.

The speed and extent of change at the genetic level would astonish researchers even a few years ago. Yoga and meditation, for example, can trigger almost immediate responses in genetic activity. Exercise, a balanced diet, good sleep, and stress reduction—all well-known for improving bodily function—exert beneficial effects via our genes. So the next frontier will be to discover how deep and lasting such changes are, how much control we have over them individually, and how they can be passed on to future generations through so-called “soft inheritance,” in which the parents’ life experiences and behavior directly influence the genome of their offspring (transmitted via the epigenome, which controls how the activities of our genes are turned up and down).

I can take a razor blade and cut a slice into my skin; this will trigger an almost immediate response in genetic activity as cells switch into repair mode, start proliferating, and move to combat potential infections. Eat some food, your gut responds. Grow older, and without even trying, there are steady changes in gene activity everywhere. Exercise, a balanced diet, good sleep, and stress reduction modify how your cells respond, this is no surprise at all, and Chopra has no special scientific knowledge to make him an authority on these effects.

But this part is a flat-out lie:

the parents’ life experiences and behavior directly influence the genome of their offspring

There are effects on development — try drinking a quart of vodka every night during a pregnancy, and yes, your behavior will affect the embryo — but no, working too hard or eating a poor diet does not change the genome you pass on to your children. There are weak correlations that show that some effects might propagate on for a generation or two via epigenetics, but they are not directed or conscious in any way, and there are many behavioral effects that confound the data. To claim that you can will changes in your genome is simply a lie.

The comments on that article are sadly gullible — I’m pretty sure Chopra wouldn’t let criticisms through. But this is truly terrible:

Can I make my cancer disappear? 2.5 cm esophicus with nothing showing in lymph nodes

No, ma’am, you can’t make a cancer disappear by consciously modifying your epigenome. The proper approach is to go to a real doctor or two, not Chopra, and listen to their recommendations. Cancers are not acts of will, punishments for sins, or subject to thoughtful consideration.

But Deepak Chopra has made a lot of money by implying that they are, and drawing in desperate, sick people who will grab onto any glimmer of hope, no matter how false.

Take the epigenome, please

Larry Moran rips into the latest hype over epigenetics. Good. There is some valuable biology buried in the field, but I see so much nonsense that even as a developmental biologist who wants to seem more attention to regulative changes in the genome, I’m just seeing so much exaggeration that I think it is doing more harm to our understanding than good (see also Carl Zimmer’s latest discussion of epigenetic over-reach). But this video is just too much.

It’s true — region of the genome can be switched on or off in a coarse way by chemical modification of DNA and associated proteins. It happens all the time. But as Larry points out, this doesn’t just happen by magic. There are regulatory factors that change patterns of gene expression, and they’re probably most responsible as well for triggering the establishment of epigenetic marks.

But here’s my objection: the hype seems to be ignoring development (I know, unforgivable). The problem with assigning too much importance to the inheritance of epigenetic marks is that individual cells and tissues acquire them throughout development and even adulthood…but they don’t matter genetically. Have the proponents never heard of Weismann’s Barrier? Changes in the somatic tissues don’t propagate to the next generation. All that matters are changes in a subset of cells in the gonads, the testes and ovaries. So we’re already dealing with a tiny fraction of our cells that also have unique tissue-specific epigenetic marks, and more importantly, their own specialized patterns of gene regulation.

Then, further, gene expression in the germ line is further refined during maturation of the egg and sperm — both of these cell types are highly specialized and gene expression is honed even more during their development. It’s nice to dream that epigenetics influences neurons in the brain, but you’re not going to inseminate anyone with your neurons, nor are those cells going to migrate down into your ovaries and pass their history on to the next generation.

The video does mention that most epigenetic marks are going to be cleared during gamete formation, and other germ-line-specific marks added, but it just blithely slides past that. It seems to me that the clearest example of epigenetic modification in inheritance is genomic imprinting, which is a consequence of differential gamete-specific modification of sperm and egg, and its main effect is in regulating gene dosage.

It’s strange. I don’t even see the appeal of these epigenetic fairy tales; I certainly don’t see any problem in evolutionary theory that requires patching up with this kind of phenomenon. But Larry includes an excerpt from an interview with the creator of the video, and suddenly all is clear. This bastardized, exaggerated version of epigenetics appeals to people who are uncomfortable with the whole central idea of modern evolutionary theory — who dislike seeing gene transmission uncoupled from the will of the individual.

I came from the world of evolutionary biology. I have always been interested in evolutionary theory but I was never convinced by the neo-Darwinian argument that environmental factors are not a big player in the generation of genetic changes. On the other hand, I never understood the fierce dismissal and often mocking of the Lamarckian ideas in schools and universities; particularly, because Darwin himself never denied Lamarck’s ideas. In epigenetics I found the mechanisms that allow you to understand the action of environmental exposures on the genome.

Whoa. That environmental factors are not a big player in the generation of genetic changes is sort of true; the environment can influence the rate of genetic changes, but doesn’t play a big role in shaping the direction of that change — that’s all a consequence of changing the frequency of representation of those changes in the population. That he brings up the idea of Lamarck is telling. Lamarckian evolution ain’t coming back, although it’s surprising how often people want it.

Also, Darwin himself never denied Lamarck’s ideas? Does he know nothing about the history of evolutionary theory? Darwin did not deny them, because his theory of inheritance was all about the inheritance of acquired characters and pangenesis, the generation of a gamete by contributions from all tissues (which, come to think of it, is what you’d need for the epigenetics hype to have any hope of working). He was pre-Mendelian genetics. He was wrong. You can’t defend Lamarck by citing a guy, no matter how influential, who had no viable theory of genetics, and who wrote in the era just before genetics was explored and understood. He might as well support it by announcing that Aristotle didn’t deny Lamarck.

As for the idea that epigenetics somehow explains the effects of environmental exposure to damaging agents…I’m trying to think of any clear examples of how that occurs, and I’m a developmental biologist who has been studying teratology for a few decades. We don’t invoke epigenetics to account for abnormal cell death, or signaling failures, or mismigration, or endocrine disruption, or any of the phenomena that are commonly responsible for non-genetic errors in development. His example is to claim that exposure to DDT in the 50s and 60s somehow led to the current high frequency of obesity.

He’s got no evidence. He has no mechanism, other than to say, “epigenetics!”

The thing to watch out for next is revealed at about 4:00 in the video, where he talks about using diet and behavior to give yourself a “healthy epigenome”, whatever that is. I’m sure some unscrupulous, dishonest someone, somewhere is writing a diet book about super-foods to super-charge your epigenome for you and your baby.

I’m calling it. There are already plenty of pseudoscientific books that mangle the concept of epigenetics. I’m sure the ones that will turn it into a marketing fad are coming up soon. We’ve already got a lot of books touting the microbiome as the cure-all for everything — I can easily imagine the fusion of the epigenome and microbiome hype machines popping up on Amazon.

Can I claim royalties for predicting it?

Give a thought to the UK today

I know, it’s hard, what with all the fireworks around here, but there’s a lesson to be learned.

After the Brexit vote, Boris Johnson resigned.

And now, another architect of the catastrophe, Nigel Farage, has stepped down.

I have to give them some credit for recognizing, after the fact, what a disaster they have engineered, but they get no respect at all for running away like cowards from the hot flaming mess they made.

Please, America, remember this: bullying, bigoted ignoramuses will disintegrate at the first hint of opposition. Keep that in mind until at least November, OK?

Oh, who am I kidding. This is an electorate with the attention span of a jellyfish.

Happy Fourth of July.

I grew up with the Vietnam war in the background. It wasn’t the hippies, or the protests, or the myth of people spitting on returning veterans that made me doubt my country: it was the National Guard raising their guns and firing into a crowd of students at Kent State. It was a duplicitous Richard Nixon resigning in disgrace. It was Henry Kissinger committing war crimes and being rewarded for it.

The Iranian hostage crisis was the dominant news item when I went off to college. It was wrong, and Iran’s descent into theocracy was a catastrophe. But what troubled me was my country’s long support for the tyrannical Shah of Iran, which had led to this crisis, the way Ronald Reagan stole credit for its resolution, and how that administration smoothly segued into total corruption, trading arms (can we stop doing that?) to Iran to shuffle money under the table to murderous right-wing killers in Nicaragua. It was Oliver North becoming the ‘brave’ face of American policy.

I’ve read the sanitized propaganda we’re given in public schools, and at the same time read the more complex histories. I hear about courageous pioneers bringing civilization west, and I read about Jeffrey Amherst and his genocidal plans, the rabble-rousing hatred that led to the massacre at Wounded Knee — and by the way, did you know that 20 medals of ‘honor’ were awarded for the murder of men, women (excuse me, ‘squaws’: wouldn’t want to humanize them), and children in that event? I lose all respect for the concept of honor. I am instructed in the heroics of the Civil War, and no one explains that the seeds of that brutality were sown in the cowardice of our noble Founding Fathers, who could talk a good game about liberty but but shied away from doing anything that might cost them some property, the human beings they owned as slaves. I had to learn on my own that we whipped around from a war to emancipate the slaves to an era of Manifest Destiny, in which plutocrats declared that they had a right to the lands of uncivilized yellow and brown people.

All my life I’ve been watching fools, criminals, and villains wrapping themselves up in their loud patriotism and being lauded for it. Do you wonder that I find flag and country tainted? Are you surprised that I find little cause to celebrate today? Do you think it’s all the fault of godless commies and leftie lies? No. It’s because the people who most thoroughly embrace that unthinking love of country do not love it for the high-minded principles stated at its founding: liberty and justice are nothing but words. They don’t love it for its past openness to immigrants; we no longer lift the lamp beside the golden door, we’re gonna build a Wall. Our Constitution isn’t about protecting our rights or guaranteeing equality, it’s about making sure every one gets to own as many guns as they want.

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