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THE ultimate guide to your genome … ‘nuf said.

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

 

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Helix as hug

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it would like like this. Yaawzaa!

Thanks Ben for the pics!

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γίνομαι

In Greek, the word genome (γίνομαι) means

“I become, I am born, to come into being”.

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Fun with memegenerator.net

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As a big fan of black and white photography, I’m intrigued by the concept of “Splitting” or so-called “black and white” thinking.  It’s something we all do to different degrees … when we avoid dealing with the “shades of gray” and group things in our life into “all good” or “all bad” groups.

Psychologists have considered this cognitive tendency to be a normal part of cognitive development (eg. good guys vs. bad guys), a response to stress, and also a part of various psychopathologies (funny, how psychiatrists have a tendency to group us into the “normal” and “abnormal”, huh?).

Is there anything wrong with seeing the world in black and white?  Perhaps, if you label mildly annoying people as “bad”, you’ll soon have no friends … but otherwise, I’m not sure.  Simplicity can be soothing.

I mean, our brains have a strong tendency to work at the extremes … for example, when it comes to cognition and movement.  We’re wired with so-called striatonigral (Go) and striatopallidal (NoGo) neural pathways that are engaged when cognition is transduced into action.  In the primal world of our ancestors, we didn’t survive very long if we danced around fretfully pondering the costs and benefits of running, or not running, from saber tooth tigers!  So, it’s no surprise, that we’re inherently uncomfortable in the wishy-washy, indecisive, muddling middle ground when making a decision.  We want to “go” or “freeze”, “do it” or “don’t”, “good” or “bad” … just make a f**king decision already.

Here’s a link to some current research on the “Go” and “NoGo” brain systems … and their genetic underpinnings (eg. the DRD2 protein is active when we are flummoxed with uncertainty which keeps us lingering in the NoGo state). Hey, our genome got us here … in one piece … it helped us stay alive … that’s not necessarily a bad thing.

thanks for the pic amadeus

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Jeans as genes

Liking the way their legs are helically intertwined.  DNA is everywhere …

photo cred to gildam (nsfw).

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If I pay to have my house fire-proofed, it creates a free economic benefit for my next-door neighbors.  If I smoke and barbecue all day long, the smoke creates an economic risk or cost for those same folks.  These are examples of what economists call “externalities … a cost or benefit, not transmitted through prices, incurred by a party who did not agree to the action“.

So, what happens if I publish my genome sequence online … does anyone else get a benefit? or incur a cost?  My children?  My siblings?  What if I were an identical twin?

Do twins favor being more similar? … in which case, maybe, they might see positive externalities?

Are the epigenomes of identical twins similar?

How does your genome influence your economic behavior?

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OK, so we have some 20,000-ish genes to help build a brain with billions of neurons and trillions of synapses … and guess what … our brains don’t work as well as we think they might.  Surprised?

Current psychological scientists suggest that there are some 19 social cognition biases, 8 memory biases, 42 decision-making biases, 35 probability-belief biases. Wow! That’s a lot of skewed thinking, not to mention concomitant stress it can generate. As a starting point to probing your own cognitive biases, check out John Grohol’s article on the 15 most common cognitive distortions:

1. Filtering.
Taking negative details and magnifying them …
2. Polarized Thinking.
Things are either “black-or-white” …
3. Overgeneralization.
Coming to a general conclusion based on a single incident …
4. Jumping to Conclusions.
Anticipate that things will turn out badly …
5. Catastrophizing.
We expect disaster to strike …
6. Personalization.
Thinking that everything is some kind of reaction to us …
7. Control Fallacies.
We see ourselves as helpless victims of fate …
8. Fallacy of Fairness.
We feel resentful because life is not fair …
9. Blaming.
We hold other people responsible for our pain …
10. Shoulds.
Rules about how others and we should behave …
11. Emotional Reasoning.
We believe that what we feel must be true automatically …
12. Fallacy of Change.
Needing to change people because our hopes depend on them …
13. Global Labeling.
Generalizing one or two qualities into a negative global judgment …
14. Always Being Right.
Having to prove that our opinions and actions are correct …
15. Heaven’s Reward Fallacy.
Expect our sacrifice and self-denial to pay off …

Oh crap …  I’m loosing it … I do (think) all of these!  Will be fun to sort out what genes relate to what biases.

[Do you know what gene regulates the initiation of new synapses?]

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Dear Diary (#1)

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Construction work at the TVA's Douglas Dam, Te...

Image by The Library of Congress via Flickr

Nope …

“On mathematical grounds, it is difficult to understand how 10-to-the-14th synaptic connections in the human brain could be controlled by a genome with approximately 10-to-the-6th genes.”

“… the classic dichotomy between “hard-wired” nativism and the “plasticity” championed by anti-nativists was woefully off the mark. Historically, “Anti-nativists”—critics of the view that we might be born with significant mental structure prior to experience—have often attempted to downplay the significance of genes by appealing to neural plasticity, viz. the brain’s resilience to damage and its ability to modify itself in response to experience, while nativists often seem to think that their position rests on downplaying (or demonstrating limits on) plasticity.”

Well, sort of … think of genes as used for pre-wiring while experience then shapes the pre-wired system.

“… it may be more profitable to draw a distinction, between prewiring and rewiring—each of which can be had in abundance without precluding the other.”

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I am (not) my phenotypes

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Probably not.  But, just in case you were wondering, it looks a lot like this.  Its (um, YOU) are a multi-level model showing overlap in genetic targets as well as signaling and neural systems between disparate latent constructs of memory and intelligence with no less than five levels of phenotype complexity (gene, signaling, neural, cognitive, and syndrome).  This super-techno-geeky-view of humanity is because:

In order to identify phenotype constructs that may ultimately be successful in genetic association studies, the field needs to move beyond the now traditional endophenotype approach and begin to build and refine multivariate multilevel phenotype models.

Check out the paper here and the super-cool PubMed exploration tools … especially PubAtlas.

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PubMed to Wordle

From a collection of my PubMed articles … link to the application.

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Little known factoid …

After writing 4 books and thousands of learned pages on the topic of evolution … all to little avail.  Charles Darwin enjoyed his elder years “shusshhing” priests whenever he had the chance.

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None of us are perfect

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