Tag Archives: evolution

Are you ready for a world without antibiotics?

[Professor Tim Walsh] “This is potentially the end. There are no antibiotics in the pipeline that have activity against NDM 1-producing enterobacteriaceae. We have a bleak window of maybe 10 years, where we are going to have to use the antibiotics we have very wisely, but also grapple with the reality that we have nothing to treat these infections with.”

And this is the optimistic view – based on the assumption that drug companies can and will get moving on discovering new antibiotics to throw at the bacterial enemy. Since the 1990s, when pharma found itself twisting and turning down blind alleys, it has not shown a great deal of enthusiasm for difficult antibiotic research. And besides, because, unlike with heart medicines, people take the drugs for a week rather than life, and because resistance means the drugs become useless after a while, there is just not much money in it.
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“The emergence of antibiotic resistance is the most eloquent example of Darwin’s principle of evolution that there ever was,” says Livermore. “It is a war of attrition. It is naive to think we can win.”

I have been writing about the huge risks we are talking with our future for years. The careless misuse of antibiotics is very costly (in human lives, in the future). Bacteria pose great risks to us. We need to take antibiotics to fight serious threats. The misuse of antibiotics by doctors, patients, agri-business… is the problem. And we are all living a much riskier future because far to little is being done to reduce the misuse of antibiotics.

More and more antibiotic treatments are losing effectiveness as bacteria evolve resistance. The evolution is accelerated by misuse. This costs lives today, but is likely to costs many thousands and hundreds of thousands and possible more in the next 50 years.

The NDM-1-producing bacteria were highly resistant to all antibiotics except tigecycline and colistin. In some cases, isolates were resistant to all antibiotics. The emergence of NDM-1 positive bacteria is potentially a serious global public health problem as there are few new anti-Gram-negative antibiotics in development and none that are effective against NDM-1.

All present-day Life on Earth Has A Single Ancestor

All present-day life arose from a single ancestor

All life on Earth shares a single common ancestor, a new statistical analysis confirms.
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Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.
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A universal common ancestor is at least 10^2,860 times more probable than having multiple ancestors, Theobald calculates.
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For his analysis, Theobald selected 23 proteins that are found across the taxonomic spectrum but have structures that differ from one species to another. He looked at those proteins in 12 species – four each from the bacterial, archaeal and eukaryotic domains of life.

Then he performed computer simulations to evaluate how likely various evolutionary scenarios were to produce the observed array of proteins. Theobald found that scenarios featuring a universal common ancestor won hands down against even the best-performing multi-ancestor models.

Very interesting. Surprising too. As the article points out this doesn’t mean all life ever on Earth evolved from the single ancestor – life that has gone extinct could be from outside this single “tree.”

Whales Evolved in the Blink of an Eye, Only 5 Million Years

Whales Evolved in the Blink of an Eye

Whales’ sizes stretch the imagination from the 100-foot (30-meter) long blue whale – the largest animal to have ever existed – to a small species about the size of a dog.
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Around 35 million years ago, when modern whales began to appear in the ocean, whale evolution ignited. Whales began as basically similar body types and evolved into everything from porpoises to blue whales over the next 5 million years, said study lead author Graham Slater of UCLA. “Five million years is like the blink of an eye,” Slater told LiveScience.

The finding supports what’s known as the explosive radiation hypothesis. The idea is that a few key traits allowed the earliest ancestors of modern cetaceans – marine mammals, including whales, dolphins and porpoises – to explore new ways of living. Once these ancestors branched out into a new body form, they stayed the course.

The key traits credited with the explosive evolution include sonar, large brains, baleen (the stringy looking stuff across some whales’ mouths that filters small animals from sea water), and complex sociality.

Trying to Find Pest Solutions While Hoping Evolution Doesn’t Exist Doesn’t Work

How To Make A Superweed

Melander wondered why some populations of scales were becoming able to resist pesticides. Could the sulfur-lime spray trigger a change in their biology, the way manual labor triggers the growth of callouses on our hands? Melander doubted it. After all, ten generations of scales lived and died between sprayings. The resistance must be hereditary, he reasoned. He sometimes would find families of scales still alive amidst a crowd of dead insects.

This was a radical idea at the time. Biologists had only recently rediscovered Mendel’s laws of heredity. They talked about genes being passed down from one generation to the next, yet they didn’t know what genes were made of yet. But they did recognize that genes could spontaneously change–mutate–and in so doing alter traits permanently.
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In the short term, Melander suggested that farmers switch to fuel oil to fight scales, but he warned that they would eventually become resistant to fuel oil as well. In fact, the best way to keep the scales from becoming entirely resistant to pesticides was, paradoxically, to do a bad job of applying those herbicides. By allowing some susceptible scales to survive, farmers would keep their susceptible genes in the scale population. “Thus we may make the strange assertion that the more faulty the spraying this year the easier it will be to control the scale the next year,” Melander predicted.
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What’s striking is how many different ways weeds have found to overcome the chemical. Scientists had thought that Roundup was invincible in part because the enzyme it attacks is pretty much the same in all plants. That uniformity suggests that plants can’t tolerate mutations to it; mutations must change its shape so that it doesn’t work and the plant dies. But it turns out that many populations of ryegrass and goosegrass have independently stumbled across one mutation that can change a single amino acid in the enzyme. The plant can still survive with this altered enzyme. And Roundup has a hard time attacking it thanks to its different shape.
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Another way weeds fight off Roundup is through sheer numbers. Earlier this year an international team of scientists reported their discovery of how Palmer amaranth resists glyphosate. The plants make the ordinary, vulnerable form of the enzyme. But the scientists discovered that they have many extra copies of the gene for the enzyme–up to 160 extra copies, in fact.
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What makes the evolution of Roundup resistance all the more dangerous is how it doesn’t respect species barriers. Scientists have found evidence that once one species evolves resistance, it can pass on those resistance genes to other species. They just interbreed, producing hybrids that can then breed with the vulnerable parent species.

Another great article from Carl Zimmer.

Poor Results on Evolution and Big Bang Questions Omitted From NSF Report

Evolution, Big Bang Polls Omitted From NSF Report by Yudhijit Bhattacharjee

The section, which was part of the unedited chapter on public attitudes toward science and technology, notes that 45% of Americans in 2008 answered true to the statement, “Human beings, as we know them today, developed from earlier species of animals.” The figure is similar to previous years and much lower than in Japan (78%), Europe (70%), China (69%), and South Korea (64%). The same gap exists for the response to a second statement, “The universe began with a big explosion,” with which only 33% of Americans agreed.

The USA continues to lag far behind the rest of the world in this basic science understanding. Similar to how we lag in other science and mathematical education. Nearly Half of Adults in the USA Don’t Know How Long it Takes the Earth to Circle the Sun.

Jon Miller, a science literacy researcher at Michigan State University in East Lansing who authored the survey 3 decades ago and conducted it for NSF until 2001. “Evolution and the big bang are not a matter of opinion. If a person says that the earth really is at the center of the universe, even if scientists think it is not, how in the world would you call that person scientifically literate? Part of being literate is to both understand and accept scientific constructs.”

I completely agree. People have the right to their opinions. But those opinions which are related to scientific knowledge (whether it is about evolution, the origin of the universe, cancer, the speed of light, polio vaccinations, multi-factorial designed experiments, magnetic fields, chemical catalysts, the effectiveness of antibiotics against viral infections, electricity, optics, bioaccumulation, etc.) are part of their scientific literacy. You can certainly believe antibiotics are affective against viral infections but that is an indication you are scientifically illiterate on that topic.

2006 NSF chapter that included the results
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South African Fossils Could be New Hominid Species

South African fossils could be new hominid species

The fossils of a female adult and a juvenile male – perhaps mother and son – are just under two million years old. They were uncovered in cave deposits at Malapa not far from Johannesburg.

Researchers tell the journal Science that the creatures fill an important gap between older hominids and the group of more modern species known as Homo, which includes our own kind. The team has assigned the name Australopithecus sediba to their finds.

“It’s at the point where we transition from an ape that walks on two legs to, effectively, us,” lead scientist Professor Lee Berger of the University of the Witwatersrand told BBC News.

“I think that probably everyone is aware that this period of time – that period between 1.8 and just over two million years [ago] – is one of the most poorly represented in the entire early hominid fossil record. You’re talking about a very small, very fragmentary record,” he explained.
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Their bones were laid down with the remains of other dead animals, including a sabre-toothed cat, antelope, mice and rabbits. The fact that none of the bodies appear to have been scavenged indicates that all died suddenly and were entombed rapidly.

“We think that there must have been some sort of calamity taking place at the time that caused all of these fossils to come down together into the cave where they got trapped and ultimately buried,” said team-member Professor Paul Dirks from James Cook University in Queensland, Australia.

All were preserved in the hard calcified clastic sediment that formed at the bottom of a pool of water.

What Dogs Reveal About Evolution

From, The Greatest Show on Earth: The Evidence for Evolution by Richard Dawkins

All breeds of dogs are domesticated wolves: not jackals, not coyotes and not foxes.
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Coppinger points out that when domestic animals break free and go feral for many generations, they usually revert to something close to their wild ancestor. We might expect feral dogs, therefore, to become rather wolf-like. But this doesn’t happen. Instead, dogs left to go feral seem to become the ubiquitous “village dogs” – “pye-dogs” – that hang around human settlements all over the Third World. This encourages Coppinger’s belief that the dogs on which human breeders finally went to work were wolves no longer. They had already changed themselves into dogs: village dogs, pye-dogs, perhaps dingos.

Real wolves are pack hunters. Village dogs are scavengers that frequent middens and rubbish dumps.
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Belyaev and his colleagues (and successors, for the experimental programme continued after his death) subjected fox cubs to standardised tests in which an experimenter would offer a cub food by hand, while trying to stroke or fondle it. The cubs were classified into three classes. Class III cubs were those that fled from or bit the person. Class II cubs would allow themselves to be handled, but showed no positive responsiveness to the experimenters. Class I cubs, the tamest of all, positively approached the handlers, wagging their tails and whining. When the cubs grew up, the experimenters systematically bred only from this tamest class.

After a mere six generations of this selective breeding for tameness, the foxes had changed so much that the experimenters felt obliged to name a new category, the “domesticated elite” class, which were “eager to establish human contact, whimpering to attract attention and sniffing and licking experimenters like dogs.” At the beginning of the experiment, none of the foxes were in the elite class. After ten generations of breeding for tameness, 18 per cent were “elite”; after 20 generations, 35 per cent; and after 30 to 35 generations, “domesticated elite” individuals constituted between 70 and 80 per cent of the experimental population.
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The tame foxes not only behaved like domestic dogs, they looked like them. They lost their foxy pelage and became piebald black and white, like Welsh collies. Their foxy prick ears were replaced by doggy floppy ears. Their tails turned up at the end like a dog’s, rather than down like a fox’s brush. The females came on heat every six months like a bitch, instead of every year like a vixen. According to Belyaev, they even sounded like dogs.

These dog-like features were side- effects. Belyaev and his team did not deliberately breed for them, only for tameness.

The famous domesticated silver fox experiment offers interesting insight into animal traits and evolution.

Prion Proteins, Without Genes, Can Evolve

‘Lifeless’ prion proteins are ‘capable of evolution’

scientists transferred prion populations from brain cells to other cells in culture and observed the prions that adapted to the new cellular environment out-competed their brain-adapted counterparts. When returned to the brain cells, the brain-adapted prions again took over the population.

Charles Weissmann, head of Scripps Florida’s department of infectology who led the study, said: “On the face of it, you have exactly the same process of mutation and adaptive change in prions as you see in viruses.

“This means that this pattern of Darwinian evolution appears to be universally active. “In viruses, mutation is linked to changes in nucleic acid sequence that leads to resistance.

“Now, this adaptability has moved one level down- to prions and protein folding – and it’s clear that you do not need nucleic acid (DNA or RNA) for the process of evolution.”
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He said: “The prion protein is not a clone, it is a quasi-species that can create different protein strains even in the same animal. “The abnormal prion proteins multiply by converting normal prion proteins.

“The implication of Charles Weissmann’s work is that it would be better to cut off that supply of normal prion proteins rather than risk the abnormal prion adapting to a drug and evolving into a new more virulent form.

Microcosm by Carl Zimmer

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cell

Cross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
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