miRNA special reprint in Nature

A while ago I had a small post about RNA interference (RNAi), linking to a really awesome and educational animation and slideshow on the topic. Again, RNAi refers to gene regulation by very small strands of RNA. There are a number of types of RNA in your cells, and a several of these are involved in RNAi: in the last post I cursorily mentioned piwi-interacting RNAs (piRNA), small interfering (siRNA) and long intergenic non-coding (lincRNA).

One type I neglected to mention is “micro” (miRNA), and this is the one about which the journal Nature has a special on-line issue. miRNA, like other types in RNAi, binds to messenger RNA in cells to prevent gene translation. The special issue of Nature focuses on miRNA in various diseases involving tumors and skeletal abnormalities, and so far as I can tell, it’s completely free to all!

What really caught my eye about this issue is its highly interactive medium, produced by some company called zmags. This “zmag” (I guess you’d call it?) has been rendered so that you view and leaf through actual magazine-like pages in your browser. I’ve got a 1+ yr old Macbook and the 2-finger zoom on the trackpad also works within the browser. Want to read and mark up some of it in your preferred program? Well you can save selected pages from the issue as a pdf, giving you flexibility in what content you download (though I did have some issues with this). A while ago I noticed Nature also used a somewhat interactive in-browser, pdf-viewing app called Readcube, though I admit I haven’t really toyed with that program.

It’s a bit challenging but also interesting to follow the possible obsolescence of the (literally) printed word. Amazon’s Kindle and other e-book platforms have all but buried the expensive, clunky hardcover tome. Academic publishers like Springer offer not only articles but also whole book chapters as pdfs available online (though they tend to require some type of university or other affiliation), and major newspapers offer most of their content on their websites.

ResearchBlogging.orgOn this topic, Carl Zimmer had a neat piece in Nature a few weeks ago about the “rise of the e-book.” He raises some excellent points regarding the pros and cons of e-books, some which I think could be extended to digital media more generally. I for one am like millions of others, relying on my handy computer and the internet for nearly all information I need to be a fully-functioning student, teacher and member of society. Still, as Zimmer points out at the end of his article, the permanence of e-books and the like is uncertain. I mean, what to do if we’re hit by another devastating Y2k?

Read on
Nature special issue here

Zimmer, C. (2011). Technology: Rise of the e-book Nature, 480 (7378), 451-452 DOI: 10.1038/480451a

Evolution: What it is and why humans aren’t immune to it

An alternate title for this post could be “BigThink Too Big For Own Britches.”

Physicist Michio Kaku (via John Hawks via Pharyngula) has re-brought my attention to the fact that a great deal of people who don’t study biology have no idea what evolution is or how it works (smart people like Kaku included). I will no further rebuke Kaku for abusing his power as a respected public figure in big Science and saying things that are outside his purview, not to mention just incorrect. His comments on biology would be like me telling high school students that the invention of the wheel or lubricants have obviated the effects of friction. Rather, I think it might be best to refresh people on what evolution is and how it works.

Quite simply, evolution is change in a gene pool. This pool could be an entire species or a small population within that species.
There are a number of ways evolution can happen. A mutation is a new genetic variant that arises in an individual, which can then be spread to later generations when that individual reproduces. A single strand of human DNA is like a string of some 3 billion letters. When a person replicates their DNA for it to be passed on to their offspring (meiosis), having to reproduce such a long strand ensures that a mistake is made at least once in a while. Hence mutations increase variation in a gene pool.
But the frequencies of genes in a population can change, that is they may become more or less common within the gene pool. This could happen by genetic drift, which is the random loss of genes. If a gene is neither adaptive nor harmful, it could simply be lost over time due to sheer chance. In contrast to mutation, drift reduces genetic variation.
If genes are adaptive or harmful, their frequency in a gene pool becomes subject to natural selection. If a gene (or set of genes) is adaptive, that means the possessor of those genes will be more likely to survive and reproduce than others. This advantage ensures the individual will pass on these genes. Over time, the adaptive genes will increase in frequency in a population. Conversely, genes that lower the likelihood of surviving and reproducing will be culled by selection. Either of these scenarios means selection is reducing genetic variation. But sometimes different forms of a gene can be adaptive in different situations or combinations, so selection will act to maintain both of these in the gene pool. So in contrast to mutation and drift, selection can reduce or maintain genetic variation.
Finally, gene flow refers to genes being introduced into a gene pool from another source. This could occur when someone from one population reproduces with an individual from another population, and so new genes may enter one of the groups. Like mutation, this will increase genetic variation in a gene pool.
Common misconceptions
It may seem counterintuitive, but evolution does not equate with progress. This is a common misconception, probably due to the social ideologies under which evolutionary theory developed. Because of selection, evolution often means that a population becomes better-suited to its environment over time, which seems like progress. But as we’ve seen above, not all evolution is selection; mutation and drift are fairly random processes of evolution that don’t necessarily bear on adaptation. In addition, environments and circumstances change, so that even if something evolved in a place where it was adaptive, it may be harmful in a new context. For example, as the earliest humans lost their body hair, they probably evolved to have darker skin: adaptive in the tropics where humans originated. But later, when early humans moved into more northerly latitudes with less ultraviolet exposure from the sun, the dark skin that was adaptive for a hairless human in a tropical environment came to hinder the body’s vitamin D synthesis: maladaptive!
Also contra popular opinion, individuals do not evolve, populations do. Trojan brand condoms recently had an ad campaign in which they encouraged men to “evolve” by using Trojan condoms when having promiscuous sex. This is in line with the incorrect idea above that ‘evolving’ means ‘becoming better’ or ‘more sophisticated.’ Of course, condoms may actually help a population to evolve: those who use condoms to prevent pregnancy are ensuring they do not pass on their genes. And if there’s any genetic predisposition to make one more likely to use condoms (and there’s not), these genes would certainly become less common in future generations. [I am NOT encouraging people not to use protection, by the way]
So this brings us to a final point: the outrageous thing (well, the main one) Dr. Kaku foolishly leashed upon an unsuspecting world is that humans are not evolving. Technology and urbanization, he tells us, has obviated natural selection on human features (well, the “gross” or visible ones). This is very wrong and shortsighted. In fact, this is one of the bases of the eugenics movement of the early 20th century. Eugenicists thought, ‘Nature is no longer ensuring some people don’t pass on their genes, so we ought to do it ourselves for the good of humankind.’ This first thought, about the insufficiency of Nature, is echoed by Dr. Kaku (surely he does not think the second).
Simply HUMANS ARE STILL EVOLVING. Remember, not all evolution = natural selection. The genetic composition of humankind is still subject to the random forces of mutation and drift. In fact, because the human population size has increased exponentially of late, the fact that there are way more people than ever means that there are more mutations entering the population, and at a faster rate, than ever! But selection is still at work, too. There are still diseases that kill people before they can pass on their genes. There are still environmental situations – even in civilized places! – that prevent people from passing on their genes.
We humans are still evolving because we are still subject to the forces of evolution, and we always will be. Now what physicist could’ve told you that?!