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For a long time, humans were pretty dumb doing little but make "the same very boring stone tools for almost 2 million years," says Philipp Khaitovich of the Partner Institute for Computational Biology in Shanghai. Then, 150,000 years ago, our big brains suddenly got smart. We started innovating. We tried different materials. We started creating art and maybe even religion. To understand what caused the cognitive spurt, researchers examined chemical brain processes known to have changed in the past 200,000 years. Comparing apes and humans, they found the most robust differences were for processes involved in energy metabolism. The finding suggests that increased access to calories spurred our cognitive advances although definitive claims of causation are premature. In most animals, the gut needs a lot of energy to grind out nourishment from food sources. But cooking, by breaking down fibers and making nutrients more readily available, is a way of processing food outside the body. Eating (mostly) cooked meals would have lessened the energy needs of our digestion systems, thereby freeing up calories for our brains. Today, humans have relatively small digestive systems and allocate around 20% of their total energy to the brain, compared to approximately 13% for non-human primates and 2-8% for other vertebrates. While other theories for the brain's cognitive spurt have not been ruled out, the finding sheds light on what made us, as Khaitovich put it, "so strange compared to other animals."

As an aside, many of our pseudogenes and other contents of “junk DNA” are thought to have been acquired by horizontal gene transfer.

The guy behind the genetically mutated guido, look at his hand. (I'm sorry you cannot un-see that)

On a more serious note, my roommate, a biology/pre-med major, found this article very interesting and said thanks.

Apparently horizontal gene transfer (or at least inserting useless bits of DNA) is not very hard to do in a lab environment and is very common in bacteria, viruses, and other single celled organisms. Here is another link I found from 08 that talks about bacteria (E.coli) if anyone wants a read http://genomebiology.com/2008/9/1/R4 (full text). Whatever I'm no expert in this field, but I like this type of stuff.

'I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.'

Well, Nature has (sort of) done this experiment already. The Fugu (pufferfish) genome has a highly 'compressed' genome, with about the same number of genes as mammals, but a much smaller complement of non-coding DNA:

http://genomebiology.com/2002/3/9/comment/1012

So it's certainly possible for an 'advanced' species to survive without the 'burden' of much of this material (obviously the regulatory elements are still required, but a lot of the highly repetitive stuff seems to be dispensable). Of course the 'junk DNA' may still confer evolutionary advantages (as the linked article put it: 'it may in fact be the clay from which evolution fashions morphogenetic changes'), and perhaps it says something that mammals have in general evolved in what most of us would regard as a much more interesting way than pufferfish...

Ehlers A, Beck S, Forbes SA, Trowsdale J, Volz A, Younger R, Ziegler A: MHC-linked olfactory receptor loci exhibit polymorphism and contribute to extended HLA/OR-haplotypes.

Genome Res 2000, 10:1968-1978.
Abstract
Full Text

The research appears focused on the genetic variation, not the resulting changes (or lack of changes) to olfaction.

There are multiple retroviral genomes in our own genome. So I am not too surprised.

http://genomebiology.com/2001/2/6/reviews/1017

The funny thing about Origin of Species is that everyone immediately was pissed that Darwin had the nerve to say that we are descendents of monkeys.

Then a few years later, people were amazed that a simple worm has 20,000 genes. <sarcasm> How could it be that such a simple lowly creature has so many genes? Isn't more better? How could humans be beat? Blasphemy! </sarcasm>

And now it's 'news' that a single cell's genome has as many genes as a human's! When will we learn that the number of genes doesn't mean 'more advanced' or 'better off'? If this single celled organism's environment caused it to evolve more genes but physically change (seemingly) very little, why are we surprised?

Same reason some source code files contain more lines of code than others. They do different things.

A better analogy is that chromosomes represent large chunks of physical memory, and the OS loader tosses code over the place.

More concretely, often one of the distinctions between closely related species is that the number of chromosomes is different, but large chunks of DNA sequence (much larger than single gene sequences) are very similar. Having large chunks of chromosome commonality is called synteny, which is strong evidence that we have common ancestry.

Here's a pic of some human-mouse synteny:
http://genomebiology.com/content/figures/gb-2005-6 -11-r92-7-l.jpg

..of antimicrobial drug resistance fall into three main types.(from genomebiology.com) First, simply develop new drugs. The post-genomic era has led to the discovery of a whole host of essential genes in bacteria whose products might represent targets for novel antimicrobial drugs. The second approach is to stop using a particular drug and reintroduce it when resistance levels have fallen. This idea derives from the assumption that resistance mechanisms come with a fitness cost and that in the absence of selection, resistant strains will be out-competed by sensitive strains. The third strategy is to learn more about the resistance mechanisms themselves. This area of research is focused on degradative enzymes and efflux pumps. see http://genomebiology.com/2005/6/13/243

Yes, for-profits like IBM and United Devices are helping, but the Proteome Folding project is not theirs. Nor do you see an pharmaceutical companies here. The ISB in a non-profit academic center. The lead scientists are top-notch. This data is being published and shared. Check out the papers at http://genomebiology.com/2004/5/8/R52 and http://www.genome.org/cgi/content/abstract/14/11/2 221 for examples. They used the Halobacterium NRC-1 as a practice run and discovered the function of a number of its unknown genes.

(For example, they uncovered over a dozen Htrs--halobacterial transducer proteins--part of the machinery halobacteria uses to sense its environment. These things are amazing extremophiles. They show how life can survive just about anywhere. They're what make the salt ponds at the south end of San Francisco Bay turn purple. NRC-1 came from the Dead Sea.)

Anyway, my point was that natural gene transfer across extremely different species (ie, cross-kingdom) isn't something completely unknown, nor is doing it necessarily some mad science perversion of nature. Whether it is a good idea or not remains to be seen and would depend on the individual case. There's a healthy medium between extreme paranoia and extreme recklessness - it would be nice to see some good regulations or necessary precautions on this, but most stuff i've heard of is from fanatics pushing on a complete ban of anything GMO. I'd agree with anyone saying Monsanto is evil, though - I'd like to see "open-source"/public domain stuff, rather than ridiculous gene patents, but that's drifting off to another topic entirely.

This is a strawman argument, anyway. The natural transfer of a genetic information across kingdoms/species/etc. is analogous to the artificial insertion of a gene into a plant, not breeding them together to produce some lame mad science experiment.

Here's a better article:

Of the 51 examined gene fusions that are represented in at least two of the three primary kingdoms (Bacteria, Archaea and Eukaryota), 31 were most probably disseminated by cross-kingdom horizontal gene transfer, whereas 14 appeared to have evolved independently in different kingdoms and two were probably inherited from the common ancestor of modern life forms.

And here is another:

The plant symbiont Bradyrhizobium japonicum has two glutamine synthetase genes, one similar to those found in other bacteria, the other 50% identical to the enzymes from higher plants. When protein sequences encoded by archaeal genomes are used to search protein sequence databases for similar sequences, some sequences have their best match with sequences from eubacteria. The opposite is also true (ref1, ref2, ref3). There are even a few cases where one sequence segment of a protein with an origin in one kingdom is attached to a segment with an origin in another kingdom (ref).

Take note that the real goal of this initiative is not to overthrow the time-tested process of peer review. Rather PLoS supporters are vested in changing the publishing process - away from the pay-per-view mentality and towards an open source type of license for scientific literature, where FULL TEXT articles can be viewed and re-distributed.

Of course the marginal costs for publishing and peer review remain. The PLoS leaders propose shifting the cost burden from readers to authors - by charging a certain fee to publish an article. Their reasoning is that since government agencies such as the NIH already pay millions of dollars for journal subscriptions within research grants, those funds could be used to subsidize the author's fees instead.

In case this sounds like "selling out" quality for profit, consider that it's in a journal's best interests to achieve prominence through a high citation rate. So quality would be ensured by recruiting high-profile scientists on editorial boards. Some journals are starting to adopt this paradigm, most notably the Journal of Biology and Genome Biology

How would journals reap profits then? By charging subscriber fees for insightful commentaries and research reviews - but still allowing free access to the fruits of publicly-funded scientific research.

Can this new crop of open source journals rival the industry behemoths? Such revolutions have already rippled through the CS, physics, and math communtities, thanks to the strong support among authors. A $20 million investment, along with a firm commitment from biomedical researchers, sounds like the kick-start needed.

The article itself and the write-up are both wrong to say that "only Genome Biology and PubMed Central" have accepted the terms of the PLOS.

• PubMed Central is a repository of papers that are published in journals. It's an NIH (US government) initiative to ensure that electronic science articles are archived permanently. It's not a journal in its own right so it doesn't really make sense to talk about it accepting their terms.
• Genome Biology is one of many journals published under the BioMed Central banner which makes primary research articles freely available online. Copyright is retained by the author. Articles are indexed in PubMed, archived in PubMed Central and metadata is harvestable through the Open Archives Initiative Protocol. There are over 40 BMC journals.

Of course, the costs of processing text and organising peer review need to be covered somehow. BMC plan to charge for non-primary content (e.g. review articles) and we are considering introducing a fee for publication (which would be waived for scientists with limited funds). The cost to the biomedical community of funding research communication by this type of fee would be an order of magnitude less than the current model of charging for access to published work.

The big advantage of making science articles open-access is that indexing is made a lot easier. A biological version of ResearchIndex (aka citeseer) would become possible. Also, you can find open-access research using Google and you don't need to be in an institution with expensive subscriptions to journals to read it.

The research article is available from the Genome Biology web site here.