Category Archives: Life Science

Synthesizing a Genome from Scratch

In the new study, scientists ordered 101 DNA fragments, encompassing the entire Mycoplasma genome, from commercial DNA synthesis companies. These fragments were designed so that each overlapped its neighboring sequence by a small amount; these overlapping stretches stick together, thanks to the chemical properties of DNA. Researchers then bound the fragments piece by piece, eventually generating the full 582,970 base pair Mycoplasma sequence.

SelFISHing

Until All the Fish Are Gone

Scientists have been warning for years that overfishing is degrading the health of the oceans and destroying the fish species on which much of humanity depends for jobs and food. Even so, it would be hard to frame the problem more dramatically than two recent articles in The Times detailing the disastrous environmental, economic and human consequences of often illegal industrial fishing.

Sharon LaFraniere showed how mechanized fishing fleets from the European Union and nations like China and Russia – usually with the complicity of local governments – have nearly picked clean the oceans off Senegal and other northwest African countries. This has ruined coastal economies and added to the surge of suddenly unemployed migrants who brave the high seas in wooden boats seeking a new life in Europe, where they are often not welcome.

The second article, by Elisabeth Rosenthal, focused on Europe’s insatiable appetite for fish – it is now the world’s largest consumer. Having overfished its own waters of popular species like tuna, swordfish and cod, Europe now imports 60 percent of what it consumes. Of that, up to half is contraband, fish caught and shipped in violation of government quotas and treaties.

I have mentioned the very serious problem of over-fishing the oceans:

The measured effects today should be enough for sensible people to realise the tragedy of the commons applies to fishing and obviously governments need to regulate the fishing to assure that fishing is sustainable. This is a serious problem exacerbated by scientific and economic illiteracy. The obvious scientific and economic solution is regulation. Determining the best regulation is tricky (and political and scientific and economic) but obviously regulation (and enforcement) is the answer.

Sadly this selfish consuming now and passing the problem to those who follow is common lately: Tax Our Children and Grandchildren Instead of Us. Remember when parents actually wanted to leave the world better off for children? What a quaint old idea.

Plants, Unikonts, Excavates and SARs

image of 4 biology supergroups

The Tree of Life Has Lost a Branch

“The results were pretty astounding. All non-bacterial life on Earth – called eukaryotic life – can now be divided into four main groups instead of the five groups that we have been working with up to now,” says Kamran Shalchian-Tabrizi, an associate professor from the University of Oslo’s Department of Biology
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All life on Earth can be divided into two essentially different life forms—eukaryotes and prokaryotes. The eukaryotes gather their genetic material in a nucleus, while the prokaryotes (bacteria and archaea) have their genetic material floating freely in the cell. Eukaryotic organisms—such as humans—can, as a result of the new findings, be divided into the following four categories:

Plants (green and red algae, and plants)
Opisthokonts (amoebas, fungi, and all animals—including humans)
Excavates (free-living organisms and parasites)
SAR (the new main group, an abbreviation of Stramenophiles, Alveolates, and Rhizaria, the names of some of its members)

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Three billion years ago, there was only bacteria and Archaea. Eukaryotic life, which comprises all multi-celled organisms, developed in the sea—probably between 1.2 and 1.6 billion years ago. It was not before about 500 million years ago that the first creatures crept onto land.

Bacteria Race Ahead of Drugs

Bacteria race ahead of drugs

Dr. Jeff Brooks has been director of the UCSF lab for 29 years, and has watched with a mixture of fascination and dread how bacteria once tamed by antibiotics evolve rapidly into forms that practically no drug can treat.
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“We are on the verge of losing control of the situation, particularly in the hospitals,” said Dr. Chip Chambers, chief of infectious disease at San Francisco General Hospital. The reasons for increasing drug resistance are well known:
– Overuse of antibiotics, which speeds the natural evolution of bacteria, promoting new mutant strains resistant to those drugs.
– Careless prescribing of antibiotics that aren’t effective for the malady in question, such as a viral infection.
– Patient demand for antibiotics when they aren’t needed.
– Heavy use of antibiotics in poultry and livestock feed, which can breed resistance to similar drugs for people.
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Terry Hazen, senior scientist at Lawrence Berkeley National Laboratory and director of its ecology program, is not at all surprised by the tenacity of our bacterial foes. “We are talking about 3.5 billion years of evolution,” he said. “They are the dominant life on Earth.”

Bacteria have invaded virtually every ecological niche on the planet. Human explorers of extreme environments such as deep wells and mines are still finding new bacterial species. “As you go deeper into the subsurface, thousands and thousands of feet, you find bacteria that have been isolated for millions of years – and you find multiple antibiotic resistance,” Hazen said.

In his view, when bacteria develop resistance to modern antibiotics, they are merely rolling out old tricks they mastered eons ago in their struggle to live in harsh environments in competition with similarly resilient species.

We have written often about the misuse of anti-biotics. This is a serious problem. And it is sad to see yet another example of well know scientific facts being ignored and by so doing threatening the healthy lives of others. i just finished a great book on bacteria and human health – Good Germs, Bad Germs.

Palm Tree Flowers After 100 Years and Self-destructs

New Genus of Self-destructive Palm found in Madagascar

It has an unusual and spectacular lifecycle; growing to dizzying heights before the stem tip converts into a giant terminal inflorescence and bursts into branches of hundreds of tiny flowers. Each flower is capable of being pollinated and developing into fruit and soon drips with nectar and is surrounded by swarming insects and birds. The nutrient reserves of the palm become completely depleted as soon as it fruits and the entire tree collapses and dies a macabre death.
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Madagascar is home to more than 10,000 plant species and 90% of Madagascar’s plants occur nowhere else in the world. The country has a highly diverse palm flora with over 170 known species, all but six of which are endemic. Scientists predict that there are less than 100 individuals of this palm in Madagascar. Only 18 percent of Madagascar’s native vegetation remains intact and a third of Madagascar’s primary vegetation has disappeared since the 1970s.

The self-destructing palm tree that flowers once every 100 years

Kew botanist Mijoro Rakotoarinivo: “It’s spectacular. It does not flower for maybe 100 years and when it’s like this it can be mistaken for other types of palm. “But then a large shoot, a bit like an asparagus, grows out of the top of the tree and starts to spread. “You get something that looks a bit like a Christmas tree growing out of the top of the palm.” There are thought to be only be 100 of the trees that are believed to be about 80 million years old.

Parasite Rex

Parasite Rex is a great book by Carl Zimmer (one of the bloggers listed in the Curious Cat directory of science blogs). This is the first book read as part of my specific plan to read more about bacteria, cells, virus, genes and the like.

One of the most enjoyable aspects of writing this blog is that I have focused much more on cool things I read. And over time the amazing things I posted about related to these topics made me realize I should put some focused effort to reading more on these topics. Some of the posts that sparked that idea: Tracking the Ecosystem Within Us – Inner Life of a Cell: Full Version – Where Bacteria Get Their Genes, People Have More Bacterial Cells than Human Cells, Biological Molecular Motors – Energy Efficiency of Digestion – Old Viruses Resurrected Through DNA – Midichloria mitochondrii – Microbes – Using Bacteria to Carry Nanoparticles Into Cells – How Bacteria Nearly Destroyed All Life – New Understanding of Human DNA – Soil Could Shed Light on Antibiotic Resistance – Symbiotic relationship between ants and bacteria

Parasite Rex was a great place to start. Carl Zimmer is a great writer, and the details on how many parasites there are and how interconnected those parasites are to living systems and how that has affected, and is affecting, us is amazing. And the next book I am reading is also fantastic: Good Germs, Bad Germs. Here is one small example from Parasite Rex, page 196-7:

A person who dies of sickle cell anemia is less likely to pass on the defective gene, and that means the disease should be exceedingly rare. But it’s not – one in four hundred American blacks has sickle sell anemia, and one in ten carries a single copy of the defective gene. The only reason the gene stays in such high circulation is that is also happens to be a defense against malaria.

Malaria is a parasite. One of the amazing things with repeated examples in the book were parasites that seemed to have extremely complicated life cycles (that don’t seem like a great strategy to prosper but obviously work). Where they grow in one life form (an insect or mammal or whatever) but must leave that life form for some other specific life form for the next stage in life (they cannot have descendants without doing so…). Seems like a crazy way to evolve but it happens over and over again.
Continue reading →

50 Species of Diatoms

Photo of diatoms by Randolph Femmer (sadly the government deleted the site, breaking the link, so I removed it).

A photomicrograph depicting the siliceous frustules of fifty species of diatoms arranged within a circular shape. The image has been inverted to white on black to bring out details. Diatoms form the base of many marine and aquatic foodchains and upon death, their glassy frustules form sediments known as diatomaceous earth.

Mapping Where Brains Store Similar Information

CMU finds human brains similarly organized

Based on how one person thinks about a hammer, a computer can identify when another person also is thinking about a hammer. It also can differentiate between items in the same category of tools, be it a hammer or screwdriver.
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The study makes two important scientific advances: “[T]here is an identifiable neural pattern associated with perception and contemplation of individual objects, and that part of the pattern is shared” by people.

The study reveals that patterns of thought extend into different regions of the brain, reflecting its complexity. It proves that a simple image can invoke thoughts in various regions of the brain, including how to use the object and experiences one has had with the object.

The study also helps to explain how the brain organizes thoughts, and the commonality of that process. “I want a complete mapping of brain states and thoughts,” Dr. Just said. “We’re taking tiny baby steps, but anything we can think about is represented in the brain.”

Lemon Tree in Japan Bears Eleven Kinds of Fruit!

A 71-year-old farmer has found a unique solution to Japan’s chronic shortage of space: grow 11 different kinds of fruit on a single tree! Manabu Fukushima of Onga, Fukuoka prefecture, combines natural horticultural skill, a lot of time and the kindness of neighbors to create one of the oddest trees you’ll ever see: a very confused Lemon tree that bears ten other citrus fruits – and Fukushima isn’t done yet!
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“Next year I want to increase the varieties,” according to the smiling farmer, and he’ll likely be true to his words based on previous success. In fact, the only thing stopping him may be a lack of suitable citrus fruit “scions” for him to graft.

DNA Seen Through the Eyes of a Coder

Great paper looking at DNA from the perspective of a computer programmer. DNA seen through the eyes of a coder by Bert Hubert:

The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 – hence the ‘bi’nary), DNA has 4 positions, T, C, G and A. Whereas a digital byte is mostly 8 binary digits, a DNA ‘byte’ (called a ‘codon’) has three digits. Because each digit can have 4 values instead of 2, an DNA codon has 64 possible values, compared to a binary byte which has 256.

A typical example of a DNA codon is ‘GCC’, which encodes the amino acid Alanine. A larger number of these amino acids combined are called a ‘polypeptide’ or ‘protein’, and these are chemically active in making a living being.
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Furthermore, 97% of your DNA is commented out. DNA is linear and read from start to end. The parts that should not be decoded are marked very clearly, much like C comments. The 3% that is used directly form the so called ‘exons’. The comments, that come ‘inbetween’ are called ‘introns’.