Tag: Biology

The X-Men Diet

The other day, I was inspired to think about creative ways to lose weight. “Creative” meaning solutions that allow one to eat tasty food. That pretty much leaves us with quackery or increasing energy expenditure. Unfortunately, quackery, being quackery, generally does not work, and increasing energy expenditure usually means doing things that are either boring (e.g., jogging) or hard work (e.g., jogging) or both (e.g., jogging).

What really increases your energy usage, isn’t boring, or hard work? Shooting energy beams from your eyes, like Cyclops[1]. Shooting energy beams from your eyes has to require lots of energy, doesn’t it. I mean, they are beams of energy. And, Cyclops always seems to be in pretty good shape. Could the two be connected? Where does the energy for the beams of energy come from? Continue reading “The X-Men Diet”

Tag, or the Springsteen-Smoke Theorem

The adrenaline rush of going fast is undeniable. The fear. The excitement. Yet, there also seems to be something redemptive about going fast, as if we can actually run away from our problems.

Well now I’m no hero
That’s understood
All the redemption I can offer, girl
Is beneath this dirty hood
–Bruce Springsteen, “Thunder Road” Continue reading “Tag, or the Springsteen-Smoke Theorem”

Fish cognition

My daughter really enjoys playing the iPad game Flick Fishing HD. Don’t worry folks. It’s all catch and release. Also, The Frogger can now identify about 30 different species of fish. We also use it for spelling practice:

Can you spell “barracuda”?

It also got me to wondering why different fish react differently to being caught on a line as this is a threat that is completely different from any natural predators. Are the fish aware they are in danger or just trying to get away from an annoyance? Is the behavior panic or some version of a standard predator avoidance? Or, is the fish evaluating the threat and then putting together the best strategy it can to counter the specific threat? That sounds pretty advanced, but we already know that some fish can use tools*.

*Depending on how you choose to define “tool”.

Coming to news stands. . .


Needless to say (but I’m going to anyway), I am pleased as punch that my lab’s most recent offering unto the body of scientific literature (“Analysis of alternative splicing associated with aging and neurodegeneration in the human brain”) was put on the cover of the current issue of Genome Research. In this paper, we investigated the connections between alternative splicing profiles in the aging brain and in brains suffering from neurodegenerative disorders, like Alzheimer’s disease. It is important to note that we were characterizing the alternative splicing differences associated with aging and disease, not identifying splicing changes that cause the diseases or the symptoms. Such questions will require ongoing work, which this study will, hopefully, help guide. Continue reading “Coming to news stands. . .”

Biological noise and the burden of proof

Yes:

But this does not change the fact that we strongly disagree with the fundamental argument put forward by Clark et al., which is that the genomic area corresponding to transcripts is more important than their relative abundance. This viewpoint makes little sense to us. Given the various sources of extraneous sequence reads, both biological and laboratory-derived (see below), it is expected that with sufficient sequencing depth the entire genome would eventually be encompassed by reads. Our statement that “the genome is not as not as pervasively transcribed as previously reported” stems from the fact that our observations relate to the relative quantity of material detected.

Of course, some rare transcripts (and/or rare transcription) are functional, and low-level transcription may also provide a pool of material for evolutionary tinkering. But given that known mechanisms—in particular, imperfections in termination (see below)—can explain the presence of low-level random (and many non-random) transcripts, we believe the burden of proof is to show that such transcripts are indeed functional, rather than to disprove their putative functionality.