Last week I posted a video of Dan Telfer arguing with his audience over who is the best dinosaur. Well, The Black Keys, a blues band from Akron, Ohio came up with the best dinosaur. His name is Frank, and he is a Funkasaurus rex. See and, more importantly, listen for yourselves. Epic dino-slide is epic. Tighten Up!
Update: the video embedding has been disabled. You can still watch it on YouTube.
Arcade Fire’s new album, The Suburbs is officially available today. Unofficially, there is already a fan video. Pretty cool. You can also listen to a stream of the entire album from NPR.
This Cincinnati group played a concert today (Thursday) at the uptown park at Oxford Ohio. A trio with Sonny on guitar, Dennis “Willy D” Williams – bass & vocals, and Dave Fair- drums & vocals. They played powerful electric blues-rock, with great covers of Blind Willie McTell, Robert Johnson and many originals. Sonny played a variety of guitars, switching between a slide lap guitar, a Debro and a Gibson Flying V. At one time he stepped off stage playing his lap guitar and let the children in the audience walk up to him and see him play. Strong blues played by a friendly band on a beautiful summer night. A great way to end the week.
Sonny showing his pickings to the younger audience at uptown Oxford, OH
Playing Crossroads Motel. Not sure where or when this was recorded:
Once again, Black Cat Zoot, whose walkin’ is always swingin’:
In case you have been vacationing in a parallel universe in the past two days, you should have heard about the new synthetic bacterium created at the J Craig Venter Institute. In a nutshell, the scientific team synthesized an artificial chromosome of the bacterium Mycoplasma mycoides and transferred it to another bacterium, Mycoplasma capricolum. The capricolum cells with the mycoides genome proved viable, and were named Mycoplasma mycoides JCVI-syn1.0. Even more briefly they synthesized Bug A’s DNA from scratch, put it in bug B, turning B into A.
I wanted to write a blog post about it. I really did. Something original, inspiring, funny, critical and deep. But so many others beat me to it, so no matter what angle I took, it’s already been covered in the last 24 hours. Informative? Yes. Debateable achievement? Yes yes, and yes. Thoughts from bigshots? Yes. Funny? totally. Religiously suspect? Verily. Government weighing in? Naturally. Reddit? Yes, even Reddit! (Thanks Shirley!)
So here’s the interview Science journal conducted with Craig Venter:
Or, if you’d rather, the Scorpions’ comment:
And the paper in Science. I’m done.
This has been going around the intertubes for a while now. Still very cool.
If the title of this post makes you cringe, then you belong to a minority of people who realize why the phrase “highly evolved” is so wrong. Unfortunately, “highly evolved” (as an absolute term) and “more evolved” (as a comparative term) seem to be used all-too frequently. They are uttered not only by non-scientists and non-biologists but even by scientists who should know better. Even when they catch themselves after blurting out “highly evolved” in a conversation (or, more embarrassingly, in a lecture), the damage is done. Yet another Freudian (Darwinian?) slip that tells of a fundamentally bad grasp on evolution. And, yes, I know, this topic has been written about by many of my betters, who are vastly more evolved better writers than I, with much better breadth and depth of knowledge of evolution, and a reach to a much wider audience.
More evolved? Source: Wikimedia commons, public domain.
So why am I writing about it? Well, this is my blog and ranting in it is my prerogative. And despite the Richard Dawkinses and Steven Jay Goulds of this world, the use of this phrase still persists. So it is up to us foot soldiers of the blogging community to do our own modest bit. If I prevent any of my six readers from being tempted to utter this phrase the next time it is (wrongly) deemed appropriate, then I have done my bit.
Why is this “highly evolved” used so much? And why is it wrong?
Consider the sponge, and then consider Albert Einstein. There are certain traits that Einstein had, that a sponge does not. We deem these traits to be of merit. Einstein developed a fundamental theory in physics. He played the violin. He ate with a knife and fork, had binocular color vision, opposable thumbs and he cultivated his facial hair in the form of a mustache.
A sponge… well, to be brief, does not have all those qualities we hold in such high merit. It kinda sits there at the bottom of the shallow ocean, flopping about, filter feeding, pooping and apparently not much else. Clearly, there are qualities to Einstein that make him more interesting than the sponge.
Less evolved? Source: Wikimedia Commons
Einstein seems, intuitively, to be more complex than a sponge, and that complexity can be quantified directly, in many ways. Actually, this is a pretty contentious point by itself: can we speak of organism complexity? Can we quantify the complexity of an organism and compare between different species? And what exactly would the complexity metric we choose tell us?
But let us assume, for argument’s sake, that our intuition that Einstein is more complex than a sponge is correct. For example, we can imagine a measure derived from the diversity and number of cells. Obviously there are more cell types in Einstein than in a sponge. Does that mean he is also more evolved? Are humans a more evolved than sponges? Chimps? After all, did life not start 3.85 billion years ago as simple and over time became more complex? Progressing, as it were from simple unicellular bacteria through more complex sponges all the way to the crowning achievement of humans? Had humans not, in a sort of (alas, Pyrrhic) victory, mastered the Earth and competed with many of earth’s species to the latter’s extinction? Isn’t competition what evolution is all about? And isn’t human victory a direct result of human complexity making humans “more evolved”? So isn’t “complexity” an end product of evolution, the more complex you are the more successful you are, and the more evolved you are?
No, no, no, no, no, and no.
The reason for this series of compounding errors is the mistaken notion that evolution by natural selection is a progression resulting in a production of increasingly complex life. Evolution is not goal oriented, and there is no teleology involved. The increasing complexity of organisms along time may seem to involve a progressive process, but there is none. It is a “statistical illusion”. What do I mean by that? Well, life did start out in less complex forms, that became more complex. But the less complex forms remained as well. Thus the distribution of complexity increased over time, but there is no directionality towards progress: the less complex life remained around as well. But over 3.85B years, complexity has had a chance to manifest itself in life, as natural selection favored some initial complexities, and those extended to become even more complex. Yes, we can trace a direct route from the first multicellular organisms, through sponges, invertebrates, vertebrates. But humans, chimps, sponges and bacteria living on Earth today are the result of exactly the same selective forces that have shaped life since it crawled out of an underwater volcano, or wherever. Complexity emerged over time, and is still emerging. But complex organisms are being added to the pool of life, rather than replacing the simple organisms. The result is an increase of a distribution of complexity levels, not the moving of an entire curve of complexity rightwards.
Apparent progress due to a to a 'wall' restricting where random change can take things. Adapted from SJ Gould. Reproduced under CC from talkorigins.org
The point I am trying to make is that humans may be more complex than sponges, but we are not “more evolved” nor are we “highly evolved”. There is no progressive process, and all of life on earth is the result of the same 3.85B years of selective pressures.
For a really good historical overview of teleological, or purpose-driven, thought in evolution, look to talkorigins.org.
Few know that Einstein was teaching evolution at Princeton. Physics was just a cover.
All of this does not mean that Highly Evolved by The Vines is not a kick-ass song. Listening to it is also a good way to get the rage from hearing “highly evolved” out of your system. Note the low complexity of the video:
Celebrate with a peanut butter and banana sandwich, while listening to The King.
Speaking of sampling bacteria, this ties in well with the previous post about GEBA. And by “well” I mean “in an alternate-universe/ altered-consciousness manner”.
The voices in the song are sampled from this KFC employee training tape. The video won a prize in machinima.com. So if you like World of Warcraft, bacteria, KFC, sampled music, or any combination of the above, you’re gonna love this.
Google flew the green-starred flag of hope yesterday, in celebration of the 150th birthday of a man who constructed a whole language based upon hope. He called himself Doctor Hopeful, and he wanted that the language he created would help break down national barriers. He made it easy to learn, so that people would be motivated to learn it as their second language. They would then speak the Language of Hope, understand each other, and not be so insular. As isolation breed suspicion, and suspicion breeds hostility and ultimately violence.
Unfortunately, neither his language nor his vision of a more understanding and tolerant mankind caught on. One hundred and fifty years after his birth, and 122 after the publication of his book, the world is no friendlier nor tolerant than it was when Ludwig Zamenhof set to correct it by publishing his book International Language: Foreword And Complete Textbook under the pseudonym of Doktoro Esperanto.
English has become the second language of choice for many. The increasing dominance of English speaking powers throughout the last 200 years resulting in English as the lingua franca is interpreted by many that English was adopted as an imposition from above. English is perceived by many who wish to preserve their non-Anglo cultures as overwhelming, a threat to their local culture, which would be diluted to extinction through constant bombardment by English speaking movies, TV shows, and Internet provided content. Zamenhof would not have liked that, as Esperanto was intended to be an adoption of choice, without carrying any threatening cultural baggage.
The Internet itself is hailed by many as a medium to strike down barriers to knowledge and help communications. But national firewalls, traffic monitoring, crackdowns on content sharing, criminal abuse and vilification in the popular media cause many to see it more as a threat to their own society, rather than a promise for all societies. And let us not forget that it is still mostly a developed world’s medium, with most of the content and cultural narrative originating from rich countries.
Neither a world-wide communication technology nor a globally dominant language seem to have brought us closer to the peaceful, understanding and egalitarian world that Zamenhof envisioned. We should be mindful of that, and of Esperanto. The Esperanto language is viewed as a curiosity at best. Esperantists as people with a quaint hobby. Happily, Esperantists do not view themselves as such. They are continuing the mission of Zamenhof for a more understanding humankind. Esperanto is kept alive by the two million who speak it, by national and international organizations, by books, magazines, and even music. Happy Birthday Doctor Hopeful.
Martin Weise of the Swedish Esperanto-singing Band Persone. from his Solo Album “more than nothing” Pli ol nenio.
In no particular order or context. No personal stuff and by no means a complete list:
WordPress (like, duh).
Wikipedia (default for looking up new stuff)
Wikis in general (great lab management tool. Don’t need LIMS)
Open Access Publishing and Creative Commons licensing.
FLOSS licensing (90% of the software I use, and 100% of what I write)
Science Bloggers (too numerous to link)
Science tweeters and FriendFeeders (too numerous to link. That’s how I keep up with things)
BLAST (Sometimes it feels like bioinformatics is should be renamed to blastology)
LaTeX (Wrote my dissertation in LaTeX, and never looked back)
OpenOffice.org (because not everyone uses LaTeX).
CiteULike (Keeping my reference library up to date and in good order)
Delicious (Keeping my bookmarks up to date and in good order)
Gmail (because finding that document you sent me a month ago would be impossible otherwise)
Google Scholar (For standing on the toes of Hobbits. Or something like that)
GIS (for blogging and making class slides)
Vim (because emacs blows)
Python (ease & power)
Biopython (OK, conflict of interest here, since I contributed a bit)
Friendly colleagues (They certainly are!)
Good students (gotta make my lab page).
Goulash for dinner. Can’t stand oven Turkey.
Music. Especially the latest song that is going around in my head:
I am preparing an introduction-to-fungi class. Found this cool Aspergillus-related animation:
Life on Earth never fails:
Not sure what this is:
Of course, there are the zombie ants I have written about before:
Seven shades of brilliant, put a big smile on my face.
All the roots hang down
Swing from town to town
They are marching around
Down under your boots
All the trucks unload
Beyond the gopher holes
There’s a world going on
Underground— Tom Waits, “Underground”
Our picture of the microbial biosphere is heavily skewed towards what we can see, culture, and are interested in. E. coli is the most touted example: a relatively rare and ineffective bug in our gut became the all-time favorite model organism, because it grows so well in a petri dish, and is easy to manipulate. Our interest in human, animal and crop pathogens is higher than our interest in bacteria that are invovled “only” in nutrient recycling, and both are studied more than those that serve no apparent function, good or bad, in our anthropocentric world.
“One percent!” is the mantra by professors teaching Microbiology 201 “we only know of 1% of the species out there!” Also, there is a whole world of bacteria that we cannot perceive: they are too rare to come up in a microscope sample, and they are too finicky to grow on E. coli‘s favorite food, LB jello. Many are physically unreachable: they live kilometers underground, or on the ocean’s bottom, in the stratosphere, or in an insurance company’s checkbook. Many are well-hidden in plain sight: there are thousands of species in a handful of soil or a bucket of seawater: how can we possibly expect to typify them all?
The idea that there is a world of life that is hitherto unknown has always seduced us. The Kraken, Mermaids, Loch-Ness monster, Bigfoot, Yeti. We are in love with the concept of life’s rarities. Very rarely, a new mammal, reptile, bird or fish is reported. That usually goes unnoticed by the mass media, unless they are unusual, (as in butt-ugly). As a rule, we are not excited by the discovery of yet another species of fish (although we should!) but more by the “freak-appeal” of that fish. It excites us that it is strange, unusual, completely different than anything we know. It makes us happy to know that sometimes life cannot be pigeonholed. Biophilia proponents might attribute this to our inherent fascination with the diversity of life, and the role it plays in our own well-being. Remember the sealed ecosystem found in Ramla, Israel three years ago? There is the appeal of the unknown: “There’s a world going on underground”. Literally, in the Ayalon Cave. Also, the rare biosphere has an evolutionary appeal: it is the crucible of genetic novelty, where new gene variants spring eternal, and through lateral gene transfer fix themselves in the non-rare microbial communities. Unlike the isolated ecosystem of the Ayalon Cave, the rare biosphere is down under our boots, and constantly feeding the “common biosphere’s” gene pool.
New albino crustacean species from Ayalon Cave
For all these reasons, when metagenomics projects started getting off the ground, there was a lot of talk and excitement about the “rare biospehere”. Finally! Finally there is a tool with which we can gather those rare microbes and study them, at least on a genomic level. We will find the bacterial albino scorpions, an archaeal Coelacanth, and maybe even a viral Sasquatch or two. We don’t have to culture them (although we’d like to), we just need enough DNA and good computational tools to help us discover the weird genes of microbial life. And we will play Tom Waits on our MP3 players while we work at it.
Initial results were amazing: there is a world going on underground. And in the ocean, an acid mine drainage, in our guts, and on our skin. Using sequences of 16S rRNA, the “barcode of bacterial life”, to estimate the number of microbial species in a sample, a slew of new species was found. Ocean samples yielded thousands of proposed new species.
However, A recent study by Quince and colleagues published in Nature Methods tells us it may be time for a reality check. The problem being that even few reads may contain multiple errors, each one leading to unique sequences, interpreted to be new species from the rare biosphere. To correct these errors, Quince and colleagues look at the flowgram: the light intensities generated by the sequencing reaction. They used their own resequenced dataset to build an error model and better assess the diversity. Their results show that sequencing errors lead to species richness estimates that are two orders of magnitude too high.
What does this mean for the rare biosphere? It is probably out there, but the distribution tail could be much shorter than we think. Another thing is: how much influence would rare species have on the combined genomes of a microbial community or ecosystem? We don’t even know that yet. The best studies we have so far in that respect are of lateral gene transfer of antibiotic resistance, and fixation of new viral strains, especially influenza. But even here, we don’t know yet how rare is “rare”.
There’s a world going on underground. We are just beginning to bumble through it though.
Sogin, M., Morrison, H., Huber, J., Welch, D., Huse, S., Neal, P., Arrieta, J., & Herndl, G. (2006). Microbial diversity in the deep sea and the underexplored “rare biosphere” Proceedings of the National Academy of Sciences, 103 (32), 12115-12120 DOI: 10.1073/pnas.0605127103
Byte Size Biology is licensed under a Creative Commons Attribution-Share Alike 3.0 Unported License.
Like this post?
