The First Artificial Cell?

June 9, 2010

Last month the news media heralded the creation in the lab of the first artificial cell. This work was a great achievement, but it wasn’t the creation of an artificial cell. What was done at the J Craig Venter Institute was the creation of an artificial bacterial  chromosome that was successfully transferred into a bacterium where it replaced the cell’s native DNA. The cell then began replicating itself making a new set of protein driven by the artificial DNA. Read a summary of this work here and the whole paper here.

This work is a great scientific advance, but it’s far from the creation of an artificial cell. The authors of this work, in fact, never claimed they had created an artificial cell. It was the press that made this leap. A synthetic genome was manufactured. And this bacterial genome was not made from scratch as the synthetic genome inserted was almost identical to that of a natural bacterium. The creation of a whole cell using only inert materials is likely a long way off. In other words, artificial life has yet to be created. Will it happen? Probably. If and when it does the achievement will be stupendous. Going to multi-cell organisms is an even more daunting challenge. But even if this is met the three basic questions facing science and indeed all human inquiry will remain:

1. How did the universe arise?
2. How did life start?
3. How did human consciousness begin?

My guess is that the answers to these three questions will remain elusive or even unattainable. But human ingenuity is as boundless as human mischief.

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Sea Levels 81,000 Years Ago

February 28, 2010

Climate scientists have used sea levels past and present to help predict those of the future. Temperature affects land ice; increased land ice will lower sea levels while the melting of this ice will raise these levels. Thus increased sea levels (secondary to ice melting) reflect a warmer global temperature. The scientific debate about what is actually happening to our climate has become super heated by politics, much of the warmth coming from scientists themselves.

To know the direction towards which the earth’s temperature is headed we have to know what it was in the past. Let’s pick 81,000 years ago. I picked this time for reasons that will be obvious as we progress. The temperature in the past is fixed and immutable though our ability to read it is always subject to amendment. To say as some do that there’s a consensus about climate change that is not debatable is to have no understanding whatsoever about how science works. Any consensus can be upended by new data or a new insight into existing data. Scientific disputes are not resolvable by a vote, their resolution depends on facts. Scientists are human, worse I can say about no man, thus they frequently get carried away with their beliefs and depart from scientific rigor just like anyone else.

Back to 81,000 years ago. According to commonplace wisdom, the earth should have been cooler then, it was well into the last glacial period, and the sea level supposedly 15 to 20 meters below today’s level. A paper in the February 12, 2010 issue of Science by geoscientists Dorale, et al challenges this view. “A speleothem that has been intermittently submerged in a cave on the island of Mallorca was dated to show that, historically, sea level was more than a meter above its present height. This data implies that temperatures were as high as or higher than now, even though the concentration of CO2 in the atmosphere was much lower.” Quotation from Science page 757.

An accompanying perspective piece by geologist R Lawrence Edwards from the University of Minnesota shows that estimating what the climate was 81,000 years ago is not a simple issue. “Dorale et al. provide evidence for high sea level at ~81,000 years ago, in the middle of the most recent 100,000-year cycle. This result challenges the observational basis for much of the discussion over recent decades… Dorale et al. dated layers of the mineral calcite, which were deposited like bathtub rings from pools of water in Mallorca caves, in the western Mediterranean. Because the pools are connected to the sea through underground passages, the layers record sea level at the time they formed. Using this approach, Dorale et al. inferred sea levels similar to modern values ~81,000 years ago. They estimated maximum rates of sea level rise of ~2 m per century. This rate is high, but not unprecedented in the geologic record. It exceeds by several times those predicted for the next century… A number of previous studies have estimated sea level ~81,000 years ago. Some of these estimates appear to agree with Dorale et al.’s findings, whereas others appear to disagree… Regardless of the ultimate verdict on sea level ~81,000 years ago, Dorale et al’s findings will stimulate ideas, discussion, and new studies of ice age history and causes.”

Note the conclusion by Edwards that new studies are needed. In assessing the current debate about climate change several questions must be answered as best we can. If the planet is warming is it doing so at historically unprecedented rates? Do we know why the change is occurring? If so, can we do anything about it? If we can, is the result worth the cost? The answers to all these questions are still uncertain.

The lay press and our politicians have failed miserably in informing the public of the facts and uncertainties of climate change. The subject is difficult and not close to being definitively settled.  People who are skeptical of man made global warning have been vilified. They have even been compared to holocaust deniers. Scientific disagreements are not resolved by ad hominem attacks.  Likening global warming skeptics to holocaust deniers is itself so anti-scientific as to be like holocaust denial. The proper response to this subject is to gather more information before changing the entire world’s economy in an effort to save the planet – a task that may prove unnecessary or impossible.

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Skeptical Science

June 3, 2008

I believe that a scientist looking at nonscientific problems is just as dumb as the next guy. Richard Feynman

When I sit on a tropical beach I like to read a fat book. Therefore, while recently on vacation, I started a big book on the history of Western science. It’s a good popular account of science from the renaissance to the present. But its introduction offers a view of the universe and of life which though typical of many scientists is profoundly unscientific.

Its introduction declares that “The Earth is and ordinary planet, the Sun is an ordinary star…and the Milky Way itself is just an ordinary galaxy.” It continues, “[A]ll you need to make human beings out of amoebas is the process of evolution by natural selection, and plenty of time.” This view of things exemplifies the trouble otherwise good scientists often get themselves into when they allow their biases to get in the way of scientific thought.

While the Earth is not at the center of the universe it seems to be at the center of life. Our inability to find life anywhere else is enough to make the Earth, Solar System, and Milky Way each extraordinary. In fact the best hypothesis about life is that it exists nowhere else in the universe. Thus we should declare that our planet, star, and galaxy are each unique rather than that they are even less than ordinary. Nevertheless, many, perhaps most, scientists hypothesize that life exists all over the universe.

The reason the first hypothesis (life is no where but on Earth) is superior to the view that life is spread throughout the universe is that is can be easily disproved while its opposite can never be dismissed. As soon as life is found somewhere else the hypothesis is finished. If you posit that life exists elsewhere in the universe not finding it today, next year, or next millennium doesn’t preclude it showing up the day after.

Enrico Fermi’s withering response to the suggestion that intelligent life existed elsewhere in the universe – to the effect of “Well where are they?” – illustrates the view that life, at least intelligent life, is unique to Earth. He was saying, in effect, that if the universe is 13 billion or so years old and if life has existed on earth for less than a billion years it should have arisen earlier than on Earth all over the universe if the development of life were a frequent event. There should be civilizations far more developed than ours all over the universe and their presence should be easily discernable because of their far advanced technologies. Since there’s no sign of them the likelihood is that they don’t exist. Thus “Where are they?”

According to my fat book on science and its ilk life is just a “complicated form of chemistry”. The best scientific thought states that life spontaneously arose about 850 million years ago. As far as we know this “complicated form of chemistry” happened just once. Yet with a sample size of one many scientists feel comfortable generalizing that it should happen any time similar or favorable conditions occur anywhere in the universe. While this is possible the odds against life spontaneously arising may be so great that if the experiment were repeated a 100 trillion or more times it would fail. Life may be a gigantic sport – an outlier so far from the norm that it is essentially a one time event. Rather than be blasé about a “complicated form of chemistry” a scientist should wonder how it ever happened. It’s a phenomenon that we understand only a little better than did Aristotle and which we have little hope of duplicating in a lab in the foreseeable future.

The three essential questions in science are how did the universe start? How did life begin? And how did human consciousness arise? To state that the transition from amoebas to humans requires nothing more than time renders the last of the three seminal problems fatuous. That it happened once does not make the jump inevitable

Again this is another experiment (the development of intelligent life) with an n of one. Anyone who has ever worked in a lab knows how easy it is to get almost any result one time. The odds against a one celled organism evolving into an animal that uses symbolic logic, builds intricate tools, and asks about its place in the cosmos may be even greater than those against the development of life itself. And to get intelligent life you first have to get life. Thus the two long shots become a sequence that may be rarer than anything else in the universe.

Scientists, who rightly declare the spontaneous generation of life to be impossible, except for the one time we know it happened, often have no trouble hypothesizing that it must be happening willy-nilly all over the universe.

The eagerness with which many scientists downgrade the Earth and Solar System to the status of a cosmic backwater seems to stem from an animus towards religion, obviously the result of the overt hostility of the altar to the lab that typifies much of the past relationship between the two. It’s as though many scientists still haven’t recovered from the shock of Galileo’s trial. The aggressive hostility expressed by many scientists to religion is distinctly antiscientific. How can science say anything about the existence of a God who exists outside of time? Yet the vast majority of scientists are vigorous, almost religious, atheists. But religion has no bearing on the statistical likelihood of life’s frequency or its uniqueness, nor is it necessary to get the universe up and running. Though science has just as much trouble getting the universe started as it does with life and consciousness. It is likely that a single satisfactory theory for the origin of the universe will never emerge. Ironically, science is as faith based as religion. At some time a scientist has to accept a starting point from which all his work derives. He takes it as a given that his starting conditions are as he assumes.

A few conclusions about life seem scientifically justifiable. The odds against life arising from inanimate matter are great – so great that it might have happened just once. Evolution follows no plan. Once a species arises its possibilities are infinite and impossible to predict. Life, once begun, does not necessarily have to evolve to intelligent life. Thus the trip from amoeba to human requires more than natural selection and time. An extraordinary amount of luck is needed. Humans are quite likely the only source of abstract thought anywhere in the cosmos. The Earth certainly occupies a special celestial place not because of its location, but because it teems with life in an otherwise outwardly dead universe. Therefore while magic is not needed to explain the universe its existence is certainly a magical metaphor.