Friday, October 29, 2004

Wee folk

The dwarf species of hominids discovered in Indonesia is getting to be a huge story. Nature has a whole web page covering many angles of the story. Most of these are free access.
The Beeb also has a litle blurb.
I missed some things of significance with my first post yesterday. The first is that these little hominids overlapped a lot with the era of anatomically modern humans, and although there is not fossil evidence of contact it is conceivable that big and little folk met each other. In this respect, it's interesting that the present-day inhabitants of Flores have lots of legends about "little folk," whom they call Ebu Gogo. It's put pretty provocatively by Henry Gee on the Nature page: maybe legends like the yeti are true as well? Maybe Boston really could win the Series. Who knows.
The second is that it's not certain who made the tools found at the site, but they are clearly reduced in size, as if intended for the smaller hominid species. It will be important to look at the hands of the skeletons. Their arms are long relative to a modern human proportions, raising the possibility that they lived in trees.

Thursday, October 28, 2004

Hobbits

A really good summary of the find of dwarf human remains on the island of Flores in Indonesia can be found at the Loom . These remains are scarcely 20,000 years old, suggesting persistent survival of multiple non-human hominids until right up to the edge of human history. (Neandertals were in the south of Spain until about 30,000 years ago.) This is completely wild, and suggests that Tolkein's Lord of the Rings was a documentary. Who knew?

The brain case of the skeleton is also very tiny, which might mean that they were less intelligent overall. However, present-day (normal sized) humans with hydrocephalus or even following surgical hemispherectomies (in both cases lacking quite a lot of brain material) are actually pretty capable people. Not to oversimplify, but software as well as hardware seems to be a part of the human intelligence package. Moreover, there were tools associated with the site, of the sort made by homo erectus.

Dwarfism in these humans may have been an adaptation to scarce resources on the island. In the same bed of bones there were dwarf elephant remains. Oh, and a little gold ring.

Wednesday, October 27, 2004

Peak experience

Our youngest son, now seven month old, crawls across the floor elbow over elbow, commando style, and uses his head as a balance point when he's clambering over cushions. Because he's not properly crawling, then, we were pretty suprised to see him reach and pull up and stand, using our television. Maybe suprised is too simple an emotion: it's a blend of pride and alarm that must be peculiar to parents with multiple kids. We had no idea he was getting ready for this!

When he gets up, he just stands there, slapping the upper surface (it's a small TV)>, his knees periodically buckling out from under him. We're the ones who aren't ready. And he's not satisfied there. He now tries pulling up on anything, from the sofas to his brothers' toy boxes, with mixed results. I caught him standing up over the crib railing last night. Yikes!

The striking thing for me is the exact species of joy on his face. He is completely focused on his new capability, so his face actually holds only the faintest of smiles. He raises his hands and slaps them down with deliberateness and even intensity. Yes really--and I know this is an infant! But his mind must be racing. He reminds me of a scientist's focus when coming across something brand new. I think the mental states must be very similar. I wouldn't be embarassed to be called childlike. Certainly my ability to keep to a schedule resembles that of one with no conception of time.

Getting down is tricky. He usually just face-plants himself off the side. Then he clambers off and starts chewing on a superhero toy, and all is right with the world again.

Lukewarm for Kerry

Kevin Drum of Washington Monthly blog goes over the big pile of Kerry endorsements at Slate. The biggest trend is how lukewarm the committed Dems seem toward him; whereas more independent Mickey Kaus and Christopher Hitchens are incrementally more passionate. Kevin and I both like Mickey's choice of words best of all-

"I'm voting for Kerry, mainly because I think Bush is prosecuting the fight against terrorism in a way that will make us dramatically less safe unless we have a conspicuous change at the top."

This seems intuitive to me, but the bulk of the Slate writers, (and a big section of electorate) have not been convinced of this. Well, there's a week still to go.
Both campaigns are wheeling out surrogates- Clinton in Pennsylvania, and, most likely Ahnold in Ohio. I think Schwarzenegger, if he shows, will have the bigger impact. I know Kerry has left African Americans unenthused, but Bill just doesn't have enough time to do his magic. Whatever you think of Schwarzenegger, he's undeniably strong with the base.
Real Clear Politics has shown a durable, albeit small, Bush average lead, and for me that means Kerry still needs to bring it if he wants to win.

Tuesday, October 26, 2004

Cassini- Huygens Mission to Saturn

In about 3 hours, Cassini-Huygens spacecraft will fly to within 200 miles of the surface of Saturn's moon Titan. Titan is really huge- bigger than Mercury or Pluto- and its atmosphere (a moon with an atmosphere!) may resemble that of the early Earth.
I do not have a full grasp of the pros and cons, but I have seen arguments that during the earliest days of the solar disk that would later become our solar system, the vicinity of Earth's current orbit would too hot to contain complex organic molecules, or evenwater (as ice). This line of thought proposes that ice and organics coalesced into planetoids further out, at Jupiter's orbit and beyond, and were much later thrown inward by the slingshot gravitational actions of the growing Jupiter and Saturn. Others were thrown out to create the current Oort cloud, the orbital source of new comets.
Thus early Earth (and early proto-life) may have been supplied with materials similar to those still in cold storage on Titan. I believe the two limitations of this scenario are that planetoid collisions with the forming Earth would have had huge energy, and would probably incinerate the kind of molecules we associate with life. Secondly, Titan has had its own geological history over the last 4 By and may be cratered or gravitationally modified. However, combined with observations of new comets I think we can get a picture of what raw materials were available on Earth during the emergence of life.

Saturday, October 23, 2004

Humans, mice... pandas thumb.

I'm getting very frustrated trying to put together a science post. Most of what I find is behind subscription walls, and I have been REALLY disappointed in the Public Access journals this time around.
What I have been trying to follow up on is the presence of repetitive DNA, which is made, up among other things, of copies of transposable elements. This DNA makes up almost 1/3 of the mouse and human genomes, with one particular family of sequences, the MaLR repetitive elements, occuring more than 380,000 times in the mouse genome! Such massive representation must confer some sort of selective advantage to outweigh the cost of keeping it. However, mammalian cells appear to be doing their darndest to suppress and control these regions of DNA by a variety of strategies.

A bit of further reading has given me two more discussion points.
The first , by Pearson et al. at Jackson Labs, shows that although these transposable elements are supressed through most of the mouse's life cycle, during the oocyte to pre-implantation embryo stages, they become very active, representing almost 3% of the total RNA output of the mature oocyte! Furthermore, the authors identify many instances of transposable elements spliced onto host mRNA transcripts, displacing elements present in the "normal" transcript made at other stages. In effect, the lunatics have taken over the asylum, at least during these developmental stages.

The second reading appears to underscore the parasitic nature of these repetitive elements. Nobrega et al. report mutant mice missing big chunks of their "gene desert" DNA, of which repetitive DNA is a part. Mice homozygous for these big genomic deletions are... perfectly normal, as far as laboratory tests can show, supporting the idea that at least a lab mouse could do pretty well without these regions. It should be said that the authors mentioned above, Pearson et al., believe that only a few transposable elements are positioned correctly to "break out" during earliest embryogenesis in the phenomena they study.

What appeals to me about this pretty confusing segment of the biological world is that it appears to be another instance of the Panda's Thumb. This notion, made famous by Stephen Jay Gould's book of the same title, states that natural selection is a master improvisor, and acts on all heritable differences without regard to human notions of elegance. As highly refined as the beings living all around us are, they followed a windy, twisty road to be here. In the case of repetitive DNA, the hosts genomes' relationship with these "parasites" makes a coevolutionary spiral in which, seemingly despite themselves, both players have benefited in their evolutionary struggles.

Quote of the day

"Somewhere, something incredible is waiting to be known." -Carl Sagan

Stolen from Cupie Spew .

Thursday, October 21, 2004

Tangled Bank is up

The 14th Tangled Bank carnival of science writings is up on Prashant Millick's web page. Go take a look! I was working on my repetitive DNA post for this carnival but I couldn't finish in time..

Wednesday, October 20, 2004

I'm doomed!

Espresso coffee raises your cholesterol levels . In that case, can I have another Krispy Kreme?

Am I repeating myself?

The sequencing of the whole animal genomes such as human and mouse has allowed quantitation of a long-established concept: that our DNA is full of repetititive sequences (Link here ; scroll down to subsection titled "Repeat content of the human genome.")This DNA does not generally code for any protein, and has been referred to as "junk DNA." In the case of humans, much of this DNA represents copies of "transposable elements" which are pieces of DNA flanked by short specialized sequences which can be "transposed," i.e. cut and pasted, copied and shuffled. These transposable elements also sometimes pick up other stretches of RNA and take them along to a new location. This might be how GLUD2 originated, for example.

A recent paper by Liu et al. shows that these transposable element derived sequences have gotten more and more enriched among primates of the human lineage. That is, the human genome is much larger than the lemur genome, and probably even expanded relative to the chimpanzee's. In the end, the human genome is at least 30% transposable element-derived sequences! That is, the shuffling and copying has been ongoing over the evolutionary interval that led to our ancestors.

Since picking a piece of DNA out of its context and putting it somewhere else is analagous to pulling out and replacing parts in a machine, it is thought that most of this activity is parasitic at best to the host genome. (In fact some human cancers may arise from somatic recombination events near these transposable elements-the link is unfortunately behind a subscription wall. ) Nevertheless, it appears that genome transposable elements have been not only tolerated, but selected for, during human evolution. Not junk at all! But for now, the selective advantages gained can only be guessed.

Sunday, October 17, 2004

How to turn a poem to sawdust

I admit it- I googled myself, and the top four hits all belong to me-- a sort of one man Google bomb . Somewhere back in the nether hits, there was this page from a state university, in which Helen Vendler takes a scalpel to Keats's poem. After a single sentence asking about the impression or theme of the poem, there is a lengthy checklist of analyses to be performed-- so long, that a quote seeking to convey the sheer tedium would get me into serious copyright trouble.
You know, if you reduce a human body to its mineral components, you get a value of about $4.50. I think something similar has happened here. I seriously doubt the people taking this course ever came up for air to look at the poem again! What seems especially wrongheaded about analyzing Keats in this way is that his whole era was a reaction to the hyper-rationalism of the Enlightenment. (I enjoy Vendler's book the Art of Shakespeare's Sonnets very much, and here I think this approach brings something. ) We scientists are often accused of hyperreductionism but I like to think that I know when to pull back on the reins.

Saturday, October 09, 2004

Public access

It bugs me that the GLUD2 article about the glutamate metabolism gene is behind a subscription wall. It's a technical paper, of course, so there's no guarantee that it would be read even if it were out in front. Still, there is a lot of cool science going on outside of spaceships and stem cells, and it would be nice if the world at large could see it. (That said, I have no idea about the workings of a sports car. To each his own?)

This past Thursday I looked over the "Journal of Record" journals, like PNAS or the Journal of Biological Chemistry I was pleasantly suprised to see these sites offering part of their current content for free. It looks like the authors have decided if it should be available, meaning that the readability for a non-expert might remain an problem. Also, did the authors have to pay?

But I'm not sure how fast biologists could go in the direction of open access. Strictly speaking, scientists do not need the subscription-only feature to their journals, and would like their work to be available to all. The role of journals, from the scientists' point of view, is to simultaneously provide a brand name (and so an immediate audience. For example I look at the Cell Press website every Thursday, and will see titles that have little to do with my narrow field) and an external standard to validate their work in the short term. That is, a Cell paper is a home run, because Cell has an ISI Impact Factor of 27, meaning more or less that the articles published in Cell tended to be cited 27 times each by subsequent work. This means that a hiring committee, looking at a young unknown with a Cell paper, can be sure that this person's work will be well received. Individuals with a longer track record can be evaluated by their own work, but the external standard function is really important for fledglings.

Switching to open access would require either the existing journals to redo their business models, or for new journals to quickly get an Impact Factor so that young people wouldn't mind sending their stuff there. At least JBC and PNAS have their toes in the water.

I will try to update this post with links to discussion of public access. I hope the links are not subscription only!!

This can't be the first occurrence of this dilemma. Any ideas out there?

UPDATE: Nature magazine has a very large set of viewpoints on their web page. I haven't read it yet but it looks extensive.

Also, Peter Suber has followed this field pretty extensively, and has comments about open access as a publishing principle, and some specifics for businesses like PLoS Biology (see my sidebar).

Without having read these yet, I am very interested in this idea of public access and curious how the costs will be borne! (See Suber.)

Saturday, October 02, 2004

Cows on mars?

A recent news item in Nature describes detection of methane in the Martian atmosphere. Methane is expected to have a short half-life on Mars, which means that something is actively making the methane-- either some kind of vulcanism, or, possibly, life. Now, as noted planetology journal The Straight Dope has pointed out, cows are a big source of the methane here on earth.
The next scientific effort will be to detect ethane, which is most consistent with living things, but I suggest going straight for the big prize. Where there's beef, there's a McDonald's. I suggest a Very Large Array (VLA) of six year-olds, which should be able to detect the Golden Arches, and therefore evidence of advanced civilization, at distances of up to several light years. They additionally could discern the play area, thus giving vital clues as to the Martians' means of locomotion.