Science

The Navajo Sandstone

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Early Jurassic
Early Jurassic

200 million years ago North America sat about 20 degrees above the equator. The newly born Mid-Atlantic Ridge was breaking Pangea apart, separating Laurentia from Gondwana, and one arm of the rift feature was  beginning to propagate through Gondwana, beginning the separation of South America as well.

Western Laurentia was a sea of sand, the remnants of which are still found all across the western USA as massive cliffs of buff colored sandstone, often over 1,000 feet high. The defining features of the Navajo Sandstone, besides its color, are the the large-scale cross-bedding and its tendency to weather across its exposed top surface into domes and rounded forms. The Navajo was one  the largest seas of sand dunes ever seen on the planet. The most spectacular exposures of the Navajo are to be seen  at Zion National Park where it reaches more than 2,500 feet in thickness. When the Colorado Plateau was uplifted in the Laramide Orogeny in last 45 million years, that created a lot of elevation difference between the uplifted ground surface and sea level, which allowed water  to  cut deeply through  the rock, exposing it to erosion. If you look at the cross section of the Grand Staircase below, you’ll see that more than a mile of rock has already been eroded from the ground above the Grand Canyon, the Vermillion Cliffs, and the White Cliffs of Navajo.

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The Sun

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From NASA TV, here’s an image of Mercury transiting the sun today:

Mercury Transit
Mercury Transit

That image gives  a good feel for the scale of the planets versus the sun. Earth would appear a little more than twice that size.  Here’s an amazing 4k time lapse video of the sun in various ultraviolet wavelengths. Based on the scale of Mercury in the image above, pick out a small feature in this video and consider the entire Earth would probably fit inside it. Then by comparison, consider the scale and the energies of the loops and streams and mass ejections in this video.

The video is even more amazing just left running in full screen on an HD monitor . It’s completely mesmerizing.

NASA Ultra-HD Video Gallery

Intelligent Design

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Sistine_Chapel

I believe in the evolution of life, I think there’s lots of fossil evidence for it and none for a single-point-of-time creation of mankind. I also believe in the evolution of the universe for the same reason. 14.5 billion years ago the universe came into existence as a hot plasma,  from which galaxies, stars and planets condensed. How simple and straightforward is that?

It could hardly be more complex. Starting with the universe, no one can explain from where the universe came or into what it is expanding. In other words, we can say “The following things have happened and here’s the evidence”. And that’s fine, I accept the evolutionary description. What’s missing is how a universe of material was born from a point in nowhere. No one  wants to talk about that and will cry “No fair!” if you try to discuss it. It is unanswerable, apparently. How does one discuss what happened or even what existed in a time before time existed? And no one wants to think about the consequences of that violating every principle of what we call science and physics. It’s too uncomfortable to confront.

Biologists will tell you life is easy to create. It seems to have existed on Earth within a few hundred million years of its formation. Provide a suitable habitat that’s warm and stable, wet with water or suitable liquid, add energy and a few raw materials like carbon and hydrogen, and bingo! you get life. We’ve been trying that for 50 years and can’t get that experiment to work. We get complex chemicals forming similar to the ones we see in life forms, but nothing that’s alive.

Something fundamental bothers me about all this. Why? There’s no answer to that question. It’s the question we seem to be asking from the moment we’re born, children ask it endlessly. Why should a universe pop into existence out of nothing? Why should life exist in it? What is the purpose of either? For all of our ability to describe what happened, we cannot answer the why of it. How could something like life come into existence from inanimate matter unless it was designed to do so? Carl Sagan famously quipped, “If you want to make an apple pie, first you must create the universe.” That’s very profound in its way. The simplest things, like a pie, require the inexplicable to have occurred, and on a scale beyond human comprehension.

In the end, it seems, I have no answers, only questions. But I reject the notion that all of this is meaningless. A universe does not exist for no reason. Life does not exist for nothing. It all exists for us to learn, to experience it. It’s where our souls grow up. It’s where our spirit evolves. That’s what I think.

 

Another step for Craig Venter.

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cell

I have previously posted about Venter’s work with synthetic organisms.

While I was digesting this new material, Craig Venter was making the Gene VII book obsolete. He set up a new company to compete with the Human Genome Project The result is well described in The Genome War by James Shreeve who was given access to Venter but less to the government funded project. This year, Venter’s autobiography was published and his plans for the future are described.

The links are at the original article which is from 2007.

Now, his group has progressed to a synthetic bacterium.

Using the first synthetic cell, Mycoplasma mycoides JCVI-syn1.0 (created by this same team in 2010), JCVI-syn3.0 was developed through a design, build, and test process using genes from JCVI-syn1.0. The new minimal synthetic cell contains 531,560 base pairs and just 473 genes, making it the smallest genome of any organism that can be grown in laboratory media. Of these genes 149 are of unknown biological function. By comparison the first synthetic cell, M. mycoides JCVI-syn1.0 has 1.08 million base pairs and 901 genes.

A paper describing this research is being published in the March 25th print version of the journal Science by lead authors Clyde A. Hutchison, III, Ph.D. and Ray-Yuan Chuang, Ph.D., senior author J. Craig Venter, Ph.D., and senior team of Hamilton O. Smith, MD, Daniel G. Gibson, Ph.D., and John I. Glass, Ph.D.

This is huge news and will take years to develop.

The most surprising result of their work—and perhaps the most sobering one for the rest of the field: The team still doesn’t understand what 31 percent of the essential genes do in even the simplest organism, to say nothing of a human genome. It’s a development Venter called “very humbling.”

“We are probably at the 1 percent level in understanding the human genome,” said Clyde Hutchison III, a distinguished professor at the Venter Institute.

That lack of knowledge isn’t standing in the way of entrepreneurs. Biology has been “hot and heavy” since the development of a molecular tool that makes gene editing easy, Hutchison explained. Scientists might be able to remove disease-causing genes or even determine a baby’s eye color. This technology, known as CRISPR/Cas-9, has alarmed many inside and outside the research community, who fear it may be used on the human genome before its effects are understood, with unforeseen results.

If he does another public seminar, I hope my friend Bradley can get me a ticket. I am now reading Lewin’s Genes XI, although he seems to be no longer the editor.

I hope I can wade through it. Sometimes, as knowledge progresses, it becomes simpler. I hope so.

“These cells would be a very, very useful chassis for many industrial applications, from medicine to biochemicals, biofuels, nutrition, and agriculture,” said Dan Gibson, a top scientist at both Venter’s research institute and his company, Synthetic Genomics Inc. Ultimately, the group wants to understand the tiny genetic framework well enough to use it as a biological foundation for more complex organisms that could address many of the world’s ills. Once each essential gene’s function is identified, scientists can build an effective computer model of it; from there, they can simulate how best to go about “adding pathways for the production of useful products,” they wrote.

I will be following this story closely, if I can only understand it.

Quote of the Day

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Charles Murray, quoting himself and Richard Herrnstein from The Bell Curve:

In sum: If tomorrow you knew beyond a shadow of a doubt that all the cognitive differences between races were 100 percent genetic in origin, nothing of any significance should change. The knowledge would give you no reason to treat individuals differently than if ethnic differences were 100 percent environmental. By the same token, knowing that the differences are 100 percent environmental in origin would not suggest a single program or policy that is not already being tried. It would justify no optimism about the time it will take to narrow the existing gaps. It would not even justify confidence that genetically based differences will not be upon us within a few generations. The impulse to think that environmental sources of difference are less threatening than genetic ones is natural but illusory.
 
In any case, you are not going to learn tomorrow that all the cognitive differences between races are 100 percent genetic in origin, because the scientific state of knowledge, unfinished as it is, already gives ample evidence that environment is part of the story. But the evidence eventually may become unequivocal that genes are also part of the story. We are worried that the elite wisdom on this issue, for years almost hysterically in denial about that possibility, will snap too far in the other direction. It is possible to face all the facts on ethnic and race differences on intelligence and not run screaming from the room. That is the essential message [pp. 314-315].