Archive for the biology Category

Blogging the "Origin of the Species"

Posted in biology, physics, Science on January 8, 2009 by Mike Procario

I read on Pharyngula about an evolutionary biologist who was planning to read the Origin of the Species for the first time. He had managed to get a Ph.D. without doing so.  This did not surprise me.

I am a physicist, but I have never read Newton’s Principia. Of course the fact that it is written in Latin is an obstacle for me. From what I have heard of it, it would be quite hard for me to follow. Even though Newton invented calculus, he did many of the proofs geometrically. Newton got the physics right, but many people have figured out better ways of explaining it.

I find evolutionary biology interesting, especially evo-devo. So much has been learned about evolution since Darwin and I think I would want the much more complete view that is available now, than you would get from the Origin of the Species.


Posted in biology, Science on October 9, 2006 by Mike Procario

Scientists in England are planning to introduce human DNA into rabbit egg cells in order to learn about how to produce stem cells. They hope that this will mitigate some of the moral objections to using human eggs.

Not So Intelligent Design

Posted in biology, Science on May 8, 2006 by Mike Procario

McGill University researchers have discovered how the enzyme Caspase-12 shuts down human immune system. Apparently 20% of people of African descent have a gene to produce this enzyme.

Caspase-12 is found in around 20% of people of African descent, but was entirely lost from all other ethnicities around 60,000 years ago.

Capase-12 blocks an enzyme involved in inflamation.

"It's possible that in Africa the protein could once have had a protective function fighting autoimmune diseases or perhaps parasites, like malaria; today caspase-12 provides no benefit to those who carry it, and often leaves the body more vulnerable to life-threatening infections and sepsis ('septic shock').

Sounds like the kind of thing that would happen if an organism were in the process of evolving and had not quite gotten there yet.

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Inherited viruses

Posted in biology, Science on April 3, 2006 by Mike Procario

There is an excellent article on endogenous retroviruses by Carl Zimmer. These are viruses that get stuck in the human genome. All viruses insert DNA into the cells' DNA so that that they hijack the cell's machinery to make more virus. Sometimes they find their way into an egg cell and do not kill the cell. In these cases the DNA is inherited by the offspring.

Scientists have discovered ways to recognize these retroviruses in the genome and found their a lot of them about 8% of the total human genome. Interesting they play an important role in evolution.

Once viruses get established in a genome, they can take any of a number of evolutionary paths. They may still be able to break out of their resident genome, become full-blown viruses, and invade another cell in the body. If they've lost the ability to become true viruses, their DNA can still get accidentally copied and inserted back into the genome. These copies may accidentally get swapped, producing drastic changes in their host's genome. And most remarkable, sometimes genes from viruses become useful to their hosts. It appears that virus genes have become vital for the development of primate placentas, and to carry out other essential tasks. While these genes retain distinctive sequences seen only in retroviruses, they show signs of having been preserved by natural selection, even as the viral genes that surround them have mutated into uselessness.


Posted in biology, physics, Science on February 4, 2006 by Mike Procario

As Kevin Drum points out switchgrass was the second most surprising thing mentioned in the State of the Union address after human-animal hybrids. I still haven’t figured that one out. A friend of mine mentioned that some friends of hers at Lawrence Berkeley National Lab were very excited by that reference since the lab has a project to turn switchgrass into methanol. I decided to see if I could find more on it so I googled switchgrass and restricted my search to   I found an article by Steven Chu, Nobel prize winner and director of Lawrence Berkeley National Lab. It appears that switchgrass is not yet a solution but LBNL is working to make it one.

In fact, we have a project that has been going on in which one takes these micro-organisms and study their genome such as to determine a pathway which lead to the digestion of the cellulose and convert it to hydrogen. However, hydrogen is not our favorite fuel, so we prefer to make ethanol or methanol. The question is: Whether can we modify the existing plants or organisms or design new ones that can directly produce energy by photosynthesis? This is yet another scientific challenge that has some hope. However, the first order of business is to mutate a standard plant, convert it into biomass, and improve the conversion of biomass into chemical energy.

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Am I Learning Some Biology?

Posted in biology, Science on January 24, 2006 by Mike Procario

I had written before that I was very impressed with Endless Forms Most Beautiful by Sean Carroll. Perhaps I have learned some biology when I read it. I was able to actually follow the post at on the number of thoracic veterbrae in mammals. It talked about Hox which were a major topic of Endless Forms, as was the concept that genes have different effects depending on when they are turned on, which is my translation of this quote.

Genes exhibit bewilderingly complex patterns of expression, and pleiotropy (the regulation of multiple phenotypic characters by a single gene) is the rule, not the exception.

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Debate on the Origin of Life

Posted in biology, Science on January 8, 2006 by Mike Procario

Joel Achenbach writes for the Washington Post. He has a humor column in the Post’s Sunday magazine, and he has a blog that is mostly humorous. So when I saw that he was writing on the origin of life I expected a satirical look at inteligent design. It was in fact a serious article mostly about Robert Hazen a scientist that is looking for the first chemicals or cells that might be classified as life in the geothermal vents deep under the sea.

Perhaps life didn’t begin at the surface of the Earth, they say, but rather deep beneath the sea around a hydrothermal vent. Such geysers form along mid-ocean ridges, spewing hot water into a dark, cold, pressurized realm that teems with bizarre organisms, like giant clams and 6-foot tube worms. The ventists say the disequilibrium between the hot and cold water is a natural driver of interesting chemical reactions. This would be a good place to cook up organic molecules from which life could emerge and evolve, they say. Moreover, the deep hydrothermal environment would have been protected from harsh ultraviolet sunlight and the meteor bombardments common at the surface of the young Earth.

Turns out that this is far from a settled question and there is a very active debate. At times it has been a very nasty debate. Hazen has described it all in a new book. In addition to informing people about this fascinating research, he is also trying to show that science is a human enterprise in hope that it will make science more accessible to nonscientists.

I fear that this example is not the best to choose, because the great success of the scienitific enterprise is that debates do get resolved, and this one is not yet settled. Science is about a set of rules about how to argue and how to collect data so that people can convince one and another that there is a correct answer. The debates can be pretty unruly until a critcal mass of high quality data can be collected.

If I were trying to show a interesting scientific debate, I would want to choose an example where there was a great disagreement and then new data was obtained from experiments or observations that clearly demonstrated that one side was right. This would be a great example of just what science is.

The problem that scientists have in explaining what we do is that once there is agreement that the correct answer has been found no one talks about the debate anymore.

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