Category: Curiosities of Nature

Oldie but goodie on junk DNA

Posted last October, Larry Moran on Junk DNA, creationism, and Ryan Gregory’s Onion test is worth a read.

A teaser:

Note that the Onion Test is for people who think they have a functional explanation for the vast amount of putative junk in our genome. What Ryan is suggesting is that such proposals should be able to account for the huge genome of onions as well as the huge genome of humans.

Let me give you some examples. Some people suggest that we need a big genome in order to protect our genes from mutation. If that’s true then why do onions need five times more DNA? Some people suggest that we have big genomes because we’re so complex and we need huge amounts of regulatory sequence. If so, why do onions need more?

Missouri legislative session is off to a solid creationist start

It’s creationism season in my back yard again. The National Center for Science Education has the goods as usual:

First, your typical equal time time bill, complete with inept politicians’ definitions of scientific terms – in defective alphabetical order, no less:

House Bill 1227, introduced in the Missouri House of Representatives on January 10, 2012, would, if enacted, require “the equal treatment of science instruction regarding evolution and intelligent design,” according to the legislature’s summary of the bill. The equal treatment provision would apply to both public elementary and secondary schools and to “any introductory science course taught at any public institution of higher education” in Missouri. Continue reading “Missouri legislative session is off to a solid creationist start”

The genome is a huge haystack. How do you find the needle?

The complexity of the machinery by which our cells run is so extreme that one of the key questions in biological research is, why doesn’t the whole thing just collapse like a house of cards in a tornado? Another way of phrasing this question is to ask, where does the information come from to keep everything running smoothly?

Consider this: the crucial task of gene regulation is carried out in large part by transcription factors, regulatory proteins that recognize and bind to very short, degenerate DNA sequences located somewhere in the rough (sometimes very rough) vicinity of genes. Once they bind, transcription factors recruit the machinery that activates their target genes. (You can also have transcription factors that repress target genes.) This is all good, until you consider the fact that a human transcription factor has to find its target sequences from among the 3 billion base pairs in the human genome. Some plant and fish transcription factors have to search through genomes with more than 100 billions base pairs. So the question is, why don’t transcription factors get lost? Where are they asking for directions?

On finding needles in the genomic haystack Continue reading “The genome is a huge haystack. How do you find the needle?”

Sometimes it is a good idea to browse through my TOC emails

… because I find stuff like this:

Hunter–gatherers and other primates as prey, predators, and competitors of snakes:

Relationships between primates and snakes are of widespread interest from anthropological, psychological, and evolutionary perspectives, but surprisingly, little is known about the dangers that serpents have posed to people with prehistoric lifestyles and nonhuman primates. Here, we report ethnographic observations of 120 Philippine Agta Negritos when they were still preliterate hunter–gatherers, among whom 26% of adult males had survived predation attempts by reticulated pythons. Six fatal attacks occurred between 1934 and 1973. Agta ate pythons as well as deer, wild pigs, and monkeys, which are also eaten by pythons, and therefore, the two species were reciprocally prey, predators, and potential competitors. Natural history data document snake predation on tree shrews and 26 species of nonhuman primates as well as many species of primates approaching, mobbing, killing, and sometimes eating snakes. These findings, interpreted within the context of snake and primate phylogenies, corroborate the hypothesis that complex ecological interactions have long characterized our shared evolutionary history.

Hating snakes is deeply ingrained in our evolutionary past. I feel validated.

Confusing data with theory

Maybe because experiments can be so much work, molecular biologists are just happy to have the data:

Krakauer, et al. “The challenges and scope of theoretical biology”, Journal of Theoretical Biology Volume 276, Issue 1, 7 May 2011, Pages 269–276:

The current absence of a strong theoretical foundation in biology means that there is weak guidance regarding what quantities or variables need to be understood to best inform a general understanding (an explanatory basis) for biological features of interest. An unfortunate result of the absence of theory is that some researchers confuse just having data with ‘understanding’. For example there is a base for collecting and analyzing the most microscopic data: experimental procedures and measurements in a high-throughput transcriptomics study are built around the assumption that transcripts are the primary data to be explained, and in neuroscience, recording from numerous individual neurons. This bias reflects a rather naive belief that the most fundamental data provide a form of explanation for a system, as if enumerating the fundamental particles were equivalent to the standard model in physics.

And here is this kind of thinking in action:

Nurse and Hayles. The cell in an era of systems biology. Cell (2011) vol. 144 (6) pp. 850-854: Continue reading “Confusing data with theory”