Category: Curiosities of Nature

Mark Ptashne on the “incoherent and counterfactual world” of epigenetics

Ptashne again cuts through epic epigenetic confusion of transcription factors versus histone marks, cause versus effect.

“The Chemistry of Regulation of Genes and Other Things”:

As I have described, where the activated gene encodes the activator itself, we have memory: a self-perpetuating state of gene expression transmitted by regulatory proteins distributed to daughter cells as cells divide.

These now obvious ideas seem to be hard to accept for some. Ignoring the specificity problem and in the search for some alternative solution to the memory problem, they have created an incoherent and counterfactual world, one in which chromatin structure determines the activity of transcription factors (recruiters) rather than the other way around. Chromatin structure is usually meant to imply histone modifications, which somehow have acquired the name epigenetic modifications. The literature is replete with studies of histone modifications presented as studies of “epigenetics,”… Continue reading “Mark Ptashne on the “incoherent and counterfactual world” of epigenetics”

Science for the People: Impossible Space

sftpThis week Science for the People is exploring the limits of science exploration in both fictional and fact. We’re joined by “lifelong space nerd” Andy Weir, to talk about his debut novel The Martian (and soon to be film, trailer below), that pits human invenitveness and ingenuity against the unforgiving environment of the red planet. And astrophysicist and science blogger Ethan Siegel returns to explore so-called “impossible space engines“, and what news stories about them can teach us about journalism and science literacy.

*Josh provides research & social media help to Science for the People and is, therefore, completely biased.

Our hunt for human-specific genes won’t explain why chimps can’t do algebra

It sounds like exciting science: the hunt for the genes that make us human. But are we learning all that much about our biology by tracking down those parts of our genome that are unique to us?

In my Pacific Standard column this week, I argue no – at least not yet. The search for human specific genes, or those parts of our genome that show signs of rapid evolution, called “human accelerated regions” hasn’t really yielded much insight into what makes us different from other species, particularly our closest relatives. For the most part, we’ve discovered genes and regulatory elements that are somehow associated with brain function, but we can’t say much more than that. Continue reading “Our hunt for human-specific genes won’t explain why chimps can’t do algebra”

How & Why to Shuffle Cards Properly

HT: David Pescovitz at BoingBoing

Midden DNA

Some people don’t like the term “junk DNA”, because they assume all that extra DNA in the human genome must be doing something. Some of those people are tenured faculty, members of the ENCODE project, and have trouble penning reasonable definitions of biological function.

Other people have experimental data to show that random sequences of DNA can be biochemically active without physiological effect, understand that the genome’s complexity resists easy classification, and can, simultaneously, understand that these swathes of non-functional DNA are valuable because they contain the history of our evolution.

In that light, I am going to propose that we abandon the misleading phrase “junk DNA” and adopt a word from archaeology used to describe piles of informative waste: midden*.

A midden…is an old dump for domestic waste which may consist of animal bone, human excrement, botanical material, vermin, shells, sherds, lithics (especially debitage), and other artifacts and ecofacts associated with past human occupation. The word is of Scandinavian via Middle English derivation, but is used by archaeologists worldwide to describe any kind of feature containing waste products relating to day-to-day human life. – Wikipedia

Now, if you want to call it midden DNA or the DNA midden, that I am happy to leave up to personal taste and style.

*A potential confusion might arise when researchers sequence DNA from biological samples in an actual midden heap – a risk with which I am willing to live.