Baby Octopi Blogging: An Aurora Update

Regular readers of my blog may remember this post on Aurora the octopus. To refresh your memory:

A month later, Aurora laid tens of thousands of eggs. Her sense of mothering was strong, despite the fact that her eggs didn’t appear to develop and aquarists eventually believed they were sterile.

Day in and day out, she sucked in water through her mantle and sent waves of cleansing water over the eggs. She defended them against hungry sea cucumbers and starfish.

I have checking from time to time to see if I can find more information on Aurora and I finally have some, slightly old (it’s dated 7/3/05) news concerning Aurora and her offspring:

Aurora’s eggs appear to have mostly hatched out with a few clusters still containing embryos still to emerge. Aurora has become more active again, often seen stretching out across the tank window. The numbers of emergent paralarvae vary daily but the end of the hatch appears in sight.

Paralarva count on May 30 – 178 babies swimming and feeding in their rearing tank and they appear to have hearty appetites.

Most of these little swimmers were transferred from a separate group of Aurora’s eggs housed in a holding tank. However, Aurora’s own egg brood also continues to emerge in view of SeaLife Center visitors. This photo shows her Monday afternoon after a short bit of activity twirling her arms and casting off old sucker disk skin. She momentarily opened up her arms widely enough to allow a better examination of a few of her many remaining unhatched eggs.

Currently, the paralarvae are eating suspended daphnia and live brine shrimp nauplii larvae periodically pulsed into the rearing tank. In addition, many of the baby octopuses are now also able to rip pieces off of small shrimp suspended in the rearing tank for a few hours. This latter food item is easy to add and remove before it becomes a mess to clean up. We are still testing and evaluating various food types recognizing that probably no single food item may be a universal diet. The oncoming challenge will be anticipating and matching different foods to the growing animals’ changing food preferences.

As for the developing paralarvae held elsewhere in the SeaLife Center, we are working with a group that now contains 90+ individuals in a rearing system designed for feeding and long-term rearing. Our aquarists report there are some that have grown larger noticeably feeding on a diet of mashed krill, Mysis shrimp and clam.
Additionally many more of Aurora’s brood have been added to an outdoor tank with natural plankton production during the long Alaska summer days to more or less fend for themselves. This group is less accessible for frequent evaluation until later in the year but may surprise us with survivors that grow and settle out of the water column to live on the tank bottom.

So apparently, as of July third Aurora was still alive! Which is good as in my last post I mentioned there was some indication that she might die. That’s one tough, determined octopus!

According to MSNBC this is an actual picture of Aurora.

And here is a series of pictures showing the development of the baby octopi.

Are they not the cutest things you have ever seen? Well, okay Aye-Ayes are cuter but these run a close second!

Why is the DNA Code Based on Codons

As everybody knows the genetic code is based on deoxyribonucleic acid (DNA). The DNA is composed of four different molecules arranged in codons with three per codon. Consequently, there are 64 possible arrangements of three molecules each. Each codon codes for one of 20 different amino acids, which in turn can make an almost infinite number of proteins. Since there are 64 arrangments but only 20 amino acids are used there is a certain amount of redundancy in the genetic code. One of the more interesting questions in genetics is how such a system developed. Recent research is beginning to answer that question.

One of quirks of the genetic code is that there are groups of codons which all translate to the same amino acid. For example, the amino acid leucine can be translated from six different codons whilst some amino acids, which have equally important functions and are translated in the same amount, have just one.

The new theory builds on an original idea suggested by Francis Crick – one of the discoverers of the structure of DNA – that the three-letter code evolved from a simpler two-letter code, although Crick thought the difference in number was simply an accident “frozen in time”.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes – but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.
By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids – explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.

“When you evolve our theory for a doublet system into a triplet system, you get an exact match up with the number and range of amino acids we see today,” said Dr van den Elsen, who has worked with Dr Stefan Babgy and Huan-Lin Wu on the theory.

One of the more interesting aspects of this is that it explains how the genetic code can maintain it’s integrity. Because, for example, translation errors can result in another amino acid with the same charactersitics. Even more interesting is it’s prediction about two amino acids (glutamine and asparagine). Both denature (or melt) at lower melting points than the other amino acids and researchers suggest that both were added somewhat later in evolution:

One possible reason for this is that the Last Universal Common Ancestor (LUCA), which evolved into all life on earth, lived in a hot sulphurous pool or thermal vent. As it moved into cooler conditions, it was able to take up these two additional amino acids and evolve into more complex organisms. This provides further evidence for the debate on whether life emerged from a hot or cold primordial soup.

Support for the theory comes from the fact that several aminoacyl-tRNA synthetases link with pairs – rather than triplettes – of bases during translation:

“There are still relics of a very old simple code hidden away in our DNA and in the structures of our cells,” said Dr van den Elsen

Which, of course, provides an avenue for future research.

I wonder what Intelligent Design advocates will make of this since it is a good example of how information content can be increased via natural selection. Something that Intelligent Design advocates say is impossible.

Is It Worth It?

It seems the goals the administration has for Iraq keep changing. It started with WMD, then changed to Sadam was an evil that had to be destroyed, went to making Iraq a shining beacon of democracy -via draining the swamp- that will change the face of the mideast. Over the last couple of weeks it has changed again, schizophrenically divided between two competing visions.

From WAPO (via Eschaton):

The United States no longer expects to see a model new democracy, a self-supporting oil industry or a society in which the majority of people are free from serious security or economic challenges, U.S. officials say.

“What we expected to achieve was never realistic given the timetable or what unfolded on the ground,” said a senior official involved in policy since the 2003 invasion. “We are in a process of absorbing the factors of the situation we’re in and shedding the unreality that dominated at the beginning.”

Administration officials still emphasize how much they have achieved despite the chaos that followed the invasion and the escalating insurgency. “Iraqis are taking control of their country, building a free nation that can govern itself, sustain itself and defend itself. And we’re helping Iraqis succeed,” President Bush said yesterday in his radio address.

Iraqi officials yesterday struggled to agree on a draft constitution by a deadline of tomorrow so the document can be submitted to a vote in October. The political transition would be completed in December by elections for a permanent government.

But the realities of daily life are a constant reminder of how the initial U.S. ambitions have not been fulfilled in ways that Americans and Iraqis once anticipated. Many of Baghdad’s 6 million people go without electricity for days in 120-degree heat. Parents fearful of kidnapping are keeping children indoors.

Barbers post signs saying they do not shave men, after months of barbers being killed by religious extremists. Ethnic or religious-based militias police the northern and southern portions of Iraq. Analysts estimate that in the whole of Iraq, unemployment is 50 percent to 65 percent.

U.S. officials say no turning point forced a reassessment. “It happened rather gradually,” said the senior official, triggered by everything from the insurgency to shifting budgets to U.S. personnel changes in Baghdad.

The ferocious debate over a new constitution has particularly driven home the gap between the original U.S. goals and the realities after almost 28 months. The U.S. decision to invade Iraq was justified in part by the goal of establishing a secular and modern Iraq that honors human rights and unites disparate ethnic and religious communities.

But whatever the outcome on specific disputes, the document on which Iraq’s future is to be built will require laws to be compliant with Islam. Kurds and Shiites are expecting de facto long-term political privileges. And women’s rights will not be as firmly entrenched as Washington has tried to insist, U.S. officials and Iraq analysts say.

We set out to establish a democracy, but we’re slowly realizing we will have some form of Islamic republic,” said another U.S. official familiar with policymaking from the beginning, who like some others interviewed would speak candidly only on the condition of anonymity. “That process is being repeated all over.”

(emphasis mine). Apparently, Cindy Sheehan’s son died so an Islamic Republic could be built in Iraq. Or maybe he died because of “…the unreality that dominated at the beginning…”. If this is too gloomy an assesment for you take comfort. There is another reason for the invasion. Also from WAPO:

Pessimists increasingly argue that Iraq may be going the way of Lebanon in the 1970s. I hope that isn’t so, and that Iraq avoids civil war. But people should realize that even Lebanonization wouldn’t be the end of the story. The Lebanese turned to sectarian militias when their army and police couldn’t provide security. But through more than 15 years of civil war, Lebanon continued to have a president, a prime minister, a parliament and an army. The country was on ice, in effect, while the sectarian battles raged. The national identity survived, and it came roaring back this spring in the Cedar Revolution that drove out Syrian troops.

One has to ask, though, if that is enough to justify this from the New York Times:

When you talk to close relatives of men and women who have been wounded in the war, it’s impossible not to notice the strain that is always evident in their faces. Their immediate concern is with the wounded soldier or marine. But just behind that immediate concern, in most cases, is the frightening awareness that they have to try and rebuild a way of life that was also blown apart when their loved one was wounded.

Ms. Olson, who is 45 and divorced, gave up everything – her work, her rented townhouse, her car – and moved from Tacoma to a hotel on the grounds of Walter Reed to be with her son and assist in his recovery.

“He was still in a coma when I got here,” she said. “He didn’t have his eyes open, and he was hooked up to all the machines. When he did open his eyes a couple of days later, he didn’t respond. His eyes didn’t follow me. That was a scary moment. But the following day his eyes started following me.”

Corporal Rosendahl has improved a great deal since those days and recently has been allowed to go with his mother on brief excursions away from the hospital. “It’s difficult for him,” Ms. Olson said. “But in those first weeks here he couldn’t move a finger. So this gives me so much hope.”

Ms. Olson is a paralegal who did work for several lawyers in Tacoma. She also worked as a claims analyst for the city’s transit system. With that work gone, she is now living on the $48 per diem she receives from the Army for food and lodging, along with money that she has reluctantly been drawing from her son’s Army pay, and assistance she is receiving from another son, Keith, who is 27.

She has also received help from charitable organizations that assist military families.

“My son is the most important thing,” she said, “and I knew that if I was going to be with him, I wouldn’t be able to meet my financial obligations.”

So she gave up the townhouse and “turned in” a Honda Accord that she had purchased just a year earlier. “Voluntary repossession,” she said.

Voluntary repossession…now that your son is of no further use you can have him back…voluntary repossession…but not before you give up your livelihood, not before you give up your house and your car…voluntary repossession…oh and here’s 48 bucks – hope it helps.
It isn’t right that so many have paid so much for so little.

The Simpsons and Religion

Last nights episode had Homer and Bart converting to Catholicism. Marge, at one point, kidnaps Bart to try and show him that Protestants can have fun too. Says Homer “why does she always interfere with my occassional interest in my children” and wants to know why he can choose his own faith. Lisa chimes in with something to the effect that everybody has the right to choose their own religion “…that’s why I choose Buddhism…” she says. A nearby catholic priest says “Yes, every child has an imaginary friend” I almost fell out of my chair I was laughing so hard at the irony.

Earth’s Early Atmosphere and the Search for Life on other Planets

Model Gives Clearer Idea Of How Oxygen Came To Dominate Earth’s Atmosphere

Researchers interested in how earth’s atmosphere came to be dominated by oxygen have come up with an interesting model to explain why there was a lag between the origin of photosynthesis and the domination of earth’s atmosphere by oxygen.

There were several processes at work. First, gasses emitted from volcanoes combined with the oxygen and acted as an oxygen sink. Second, oxidation of iron from space bombardment acted as a second sink. Researcers found that varying the estimates of iron content in the earth’s crust could change the time frame by up to a billion years in one direction or the other.

Here is how it works:

Earth’s oxygen supply originated with cyanobacteria, tiny water-dwelling organisms that survive by photosynthesis. In that process, the bacteria convert carbon dioxide and water into organic carbon and free oxygen. But Claire noted that on the early Earth, free oxygen would quickly combine with an abundant element, hydrogen or carbon for instance, to form other compounds, and so free oxygen did not build up in the atmosphere very readily. Methane, a combination of carbon and hydrogen, became a dominant atmospheric gas.

With a sun much fainter and cooler than today, methane buildup warmed the planet to the point that life could survive. But methane was so abundant that it filled the upper reaches of the atmosphere, where such compounds are very rare today. There, ultraviolet exposure caused the methane to decompose and its freed hydrogen escaped into space, Claire said.

The loss of hydrogen atoms to space allowed increasingly greater amounts of free oxygen to oxidize the crust. Over time, that slowly diminished the amount of hydrogen released from the crust by the combination of pressure and temperature that formed the rocks in the crust.

“About 2.4 billion years ago, the long-term geologic sources of oxygen outweighed the sinks in a somewhat permanent fashion,” Claire said. “Escaping to space is the only permanent escape that we envision for the hydrogen, and that drove the planet to a higher oxygen level.”

The most intersting part of the article is the last sentence:

“There is interest in this work not just to know how an oxygen atmosphere came about on Earth but to look for oxygen signatures for other Earth-like planets,” Claire said.

Note that the one thing missing in this search for life on other planets is Intelligent Design

I’m All Alone…

I’m all alone, there’s no one here beside me,
My troubles are all gone, there’s no one here to deride me…”

I’ve been getting over 200 hits a day lately, but few comments outside of a small group of great people. So I just thought I would mention that I do like comments and try to respond to each and every one of them. Really, it’s okay, I don’t bite!

I also just noticed that I have received over 20,000 visitors since I started this site (which is a heck of a lot more than what I thought I’d have so (imagine this next bit in your best Eyore voice):

Thanks for noticing, I’m just grateful for the attention, don’t leave any comments if you don’t feel like it, I’m just happy to have you visit. I don’t really need comments…

Have I whined enough yet?

Life is Sooo Unfair

Do to some recent feedback on my Naked Mole Rat posts I thought there might be a way of making some money off of it – maybe millions – so I could retire in style. My first thought was I could create a Naked Mole Rat stuffed animal or maybe a beanie baby (could you imagine the reaction of some kid pulling one of these ugly spuds out of a toy meal?). But then I found this:

from here

Oh well, back to the drawing board.