Posts about evolution

Scientists Watch Single Cell Organisms Evolve Multicellular Trait in Response to Predation

The scientists used the ciliate predator Paramecium tetraurelia to select for the de novo evolution of multicellularity in outcrossed populations of C. reinhardtii. They show that multicellular life cycles that evolved were passed on to future generations (the change was heritable). The evolved multicellular life cycles are stable over thousands of asexual generations in the absence of predators. Because C. reinhardtii has no multicellular ancestors, these experiments represent a novel origin of multicellularity.

De novo origins of multicellularity in response to predation

Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations.

The control populations remained unicellular. The populations subjected to predation evolved in different ways including one that formed stereotypic eight-celled clusters (Fig. 1A), with an apparent unicellular and tetrad life stage.

electron microscope images of multicellular colonies from evolved populations

Scanning electron micrographs of representative multicellular colonies from evolved populations. (A) Shows an amorphous cluster from population B2. Cell number varies greatly between clusters in this clone and between clones in this population. (B) Shows an eight-celled cluster from population B5. Octads were frequently observed in both populations.

an external membrane is visible around both evolved multicellular colonies, indicating that they formed clonally via repeated cell division within the cluster, rather than via aggregation.

The article also provides details on the scientific inquiry process where theory meets practical realities of observation. I think these ideas are very important and we often gloss over such details. This article was shared as an open access article and is written so that those who are interested in science but are not scientists can understand, which is a valuable. The research was funded by USA National Science Foundation, the John Templeton Foundation, the NASA Astrobiology Institute, a NASA Postdoctoral Program Fellowship and a Packard Foundation Fellowship. And the researchers work at public and private universities. Such research should all be published in an open access manner.

Related: The Amazing Reality of Genes and The History of Scientific InquiryParasite Evolved from Cnidarians (Jellyfish etc.)Why Don’t All Ant Species Replace Queens in the Colony, Since Some DoScientific Inquiry Leads to Using Fluoride for Healthy TeethMechanical Gears Found in Jumping Insects

The Amazing Reality of Genes and The History of Scientific Inquiry

cover of The Gene

The Gene by Siddhartha Mukherjee is a wonderful book. He does a great job of explaining the history of scientists learning about genes as well as providing understandable explanations for the current scientific understanding of genes and how they impact our lives.

As I have mentioned before, I find biology fascinating even though I found biology classes utterly boring and painful. I wish everyone could learn about biology with the insight people like Siddhartha Mukherjee provide. I realize not everyone is going to find the history and understanding of genes to be fascinating but for those who might this book is a great read. And don’t rule the idea out just because you found biology classes painful.

Life may be chemistry, but it’s a special circumstance of chemistry. Organisms exist not because of reactions that are possible, but because of reactions that are barely possible. Too much reactivity and we would spontaneously combust. Too little, and we would turn cold and die. Proteins enable these barely possible reactions, allowing us to live on the edges of chemical entropy – skating perilously, but never falling in.
– page 134

Whether it is the physics of our solar system or our biology there is a precarious band that allowed beings such as ourselves to evolve.

most genes, as Richard Dawkins describes them, are not “blueprints” but “recipes.” They do not specify parts, but processes; they are formulas, not forms. If you change a blueprint, the final product is change in a perfectly predictable manner: eliminate a widget specified in the plan, and you get a machine with a missing widget. But alteration of a recipe or formula doesn’t not change the product in a predictable manner: if you quadruple the amount of butter in a cake, the eventual effect is more complicated than just a quadruply buttered cake (try it; the whole thing collapses in an oily mess).
– page 454

The is a powerful idea. And when combined with turning genes on and off it is understandable how complex determining genetic impacts on biology and disease are. A few diseases or results (e.g. blue eyes) are nearly as simple as 1 or a few genes being altered in a specific way but most are not nearly so easy. And it isn’t like even that is so easy but with the amazing efforts scientists have made and the advanced tools those scientists created it can now seem simple to identify some such diseases.

The genetic code is universal. A gene from a blue whale can be inserted into a microscopic bacterium and it will be deciphered accurately and with near perfect fidelity. A corollary: there is nothing particularly special about human genes.
– page 480

This is something I have known and understood but it is still amazing. Genes and proteins and how they act to create the incredible diversity of life is something that is awe inspiring.

This book is a wonderful adventure for those interested in life and scientific inquiry.

Related: Epigenetics, Scientific Inquiry and UncertaintyHuman Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticUnexpected Risks Found In Editing Genes To Prevent Inherited DisordersEpigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeWhy Don’t All Ant Species Replace Queens in the Colony, Since Some Do

Dinosaur Bird Wing and Feather in Amber

Rare Dinosaur-Era Bird Wings Found Trapped in Amber

Two tiny wings entombed in amber reveal that plumage (the layering, patterning, coloring, and arrangement of feathers) seen in birds today already existed in at least some of their predecessors nearly a hundred million years ago.

Skin, muscle, claws, and feather shafts are visible, along with the remains of rows of feathers similar in arrangement and microstructure to modern birds.

photo of dinosaur wing in amber with feathers visible

The nearly 100 million year old wing shows a structure that is very similar to modern birds.

The piece in this photo, and others samples, were bought at an amber market in Myitkyina, the capital of Kachin state in northern Myanmar. The region is politically unstable and most of the amber is sold to Chinese consumers for jewelry and decorative carvings.

Read the related posts for more on the wonderful discoveries saved in amber of hundreds of millions of years. We get to read about these amazing discoveries so often it is easy to lose appreciation for how amazing each one is. This photo shows a wind that was used by a dinosaur almost 100 million years ago.

Related: Marine Plankton From 100 Million Years Ago Found in Amber 2008)Learning About Life over 200 Million Years Ago From Samples Trapped In Amber (2012)The evolution of birds from small predatory dinosaursDino-Era Feathers Found Encased in Amber (2008)Amber Pieces Containing Remains from Dinosaurs and Birds Show Feather Evolution (2011)Ancient Whale Uncovered in Egyptian Desert

Our Poor Antibiotic Practices Have Sped the Evolution of Resistance to Our Last-Resort Antibiotic

The risk to human health due to anti-biotic resistance continues to be a huge public health concern. Our continued failure to adopt better antibiotics practices increase that risk. Those bad practices include feeding large amounts of antibiotics to farm animals to increase yields and increase the evolution of drug resistant bacteria.

Resistance to last-resort antibiotic has now spread across globe

The genes found in Denmark and China are the same, says Aarestrup, suggesting mcr-1 has travelled, rather than arising independently in each place. It is thought to have emerged originally in farm animals fed colistin as an antibiotic growth promoter.

In 2012, the World Health Organization called colistin critically important for human health, meaning its use in animals should be limited to avoid promoting resistance. Yet in 2013, the European Medicines Agency reported that polymyxins were the fifth most heavily used type of antibiotic in European livestock.

Colistin, an antibiotic that previously was a last defense against resistant strains of bacteria, is even more heavily used in China than Europe (it is not clear how the resistance developed but it likely developed in one place, most likely China, and spread rather than emerging in 2 places). The USA has been more responsible and has not risked human health through the widespread use of colistin in farm animals. But the USA still uses antibiotics irresponsibly to promote livestock growth at the risk of human lives being lost as antibiotics lose their effectiveness as bacteria evolve resistance (which is sped by poor practices in agri-business).

Antibiotic resistance is an enormous risk to human health. Millions of lives could be lost and we have have years to reduce those risks. Scientists are doing a great deal of work to find new tools to help us avoid catastrophe but we have been far too careless in our practices, especially in the massive use of antibiotics merely to boost yields in agribusiness.

Related: Are you ready for a world without antibiotics? (2010)80% of the Antibiotics in the USA are Used in Agriculture and AquacultureWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Waste Treatment Plants Result in Super Bacteria (2009)CDC Again Stresses Urgent Need to Adjust Practices or Pay a Steep Price (2013)

Parasite Evolved from Cnidarians (Jellyfish etc.)

This is another instance of science research providing us interesting details about the very odd ways life has evolved on earth.

Genome sequencing confirms that myxozoans, a diverse group of microscopic parasites that infect invertebrate and vertebrate hosts, are actually highly reduced cnidarians — the phylum that includes jellyfish, corals and sea anemones.

“This is a remarkable case of extreme degeneration of an animal body plan,” said Paulyn Cartwright, associate professor of ecology and evolutionary biology at the University of Kansas (KU) and principal investigator on the research project. “First, we confirmed they’re cnidarians. Now we need to investigate how they got to be that way.”

images of myxozoans parasite spores and a jellyfish

Not only has the parasitic micro jellyfish evolved a stripped-down body plan of just a few cells, but via data generated at the KU Medical Center’s Genome Sequencing Facility researchers also found the myxozoan genome was drastically simplified.

“These were 20 to 40 times smaller than average jellyfish genomes,” Cartwright said. “It’s one of the smallest animal genomes ever reported. It only has about 20 million base pairs, whereas the average Cnidarian has over 300 million. These are tiny little genomes by comparison.”

Despite its radical phasedown of the modern jellyfish’s body structure and genome over millions of years, Myxozoa has retained the essential characteristic of the jellyfish — its stinger, or “nematocyst” — along with the genes needed to make it.

“Because they’re so weird, it’s difficult to imagine they were jellyfish,” she said. “They don’t have a mouth or a gut. They have just a few cells. But then they have this complex structure that looks just like stinging cell of cnidarian. Jellyfish tentacles are loaded with them — little firing weapons.”

The findings are the stuff of scientific fascination but also could have a commercial effect. Myxozoa commonly plague commercial fish stock such as trout and salmon.

“They’re a very diverse group of parasites, and some have been well-studied because they infect fish and can wreak havoc in aquaculture of economic importance,” Cartwright said.

Continue reading

Cancer Rates Consistent Across Species Instead of Increasing Due to Body Mass

It would seem sensible to think cancer should be more prevalent in species with a huge number of cells, and thus more cells to become cancerous. But cancer risk doesn’t increase in this way. This interesting, open source paper, sheds some light on what is behind this.

Solutions to Peto’s paradox revealed by mathematical modelling and cross-species cancer gene analysis

Whales have 1000-fold more cells than humans and mice have 1000-fold fewer; however, cancer risk across species does not increase with the number of somatic cells and the lifespan of the organism. This observation is known as Peto’s paradox. How much would evolution have to change the parameters of somatic evolution in order to equalize the cancer risk between species that differ by orders of magnitude in size? Analysis of previously published models of colorectal cancer suggests that a two- to three-fold decrease in the mutation rate or stem cell division rate is enough to reduce a whale’s cancer risk to that of a human. Similarly, the addition of one to two required tumour-suppressor gene mutations would also be sufficient.

We surveyed mammalian genomes and did not find a positive correlation of tumour-suppressor genes with increasing body mass and longevity. However, we found evidence of the amplification of TP53 in elephants, MAL in horses and FBXO31 in microbats, which might explain Peto’s paradox in those species. Exploring parameters that evolution may have fine-tuned in large, long-lived organisms will help guide future experiments to reveal the underlying biology responsible for Peto’s paradox and guide cancer prevention in humans.

Elephants in Kenya

Elephants in Kenya by John Hunter. See more photos from my trip to Kenya.

In another way it would make sense that large animals would have hugely increased risks of cancer. As they evolved, extremely high cancer rates would be a much bigger problem for them. Therefore it wouldn’t be surprising to find they have evolved a way of reducing cancer risks.

Despite these limitations, we found genes that have been dramatically amplified in specific mammalian genomes, the most interesting of which is the discovery of 12 TP53 copies in the genome of the African elephant. We subsequently cloned those genes and identified 19 distinct copies of TP53 in African elephants and 15–20 in Asian elephants [1]. Another potential lead for solving Peto’s paradox is MAL, which is found to have eight copies in the horse genome and two in microbat. This could be an example of convergent evolution where a large animal (horse) and a small, long-lived animal (microbat) both evolved extra copies of the same gene to overcome their increased risk of cancer. Further analysis and experimentation would need to be performed to determine the function of these copies and whether or not they provide enhanced suppression of carcinogenesis.

The researchers have found an interesting potential explanation for how that has been accomplished.

Related: The Only Known Cancerless Animal (the naked mole rat)Webcast of a T-cell Killing a Cancerous CellResearchers Find Switch That Allows Cancer Cells to SpreadCancer Vaccines

Refusal to Follow Scientific Guidance Results in Worms Evolving to Eat Corn Designed to Kill The Worms

An understanding of natural selection and evolution is fundamental to understanding science, biology, human health and life. Scientists create wonderful products to improve our lives: vaccines, antibiotics, etc.; if we don’t use them or misuse them it is a great loss to society.

There is also great value in genetic enhanced seeds and thus plants (through natural human aided processes such as breeding and providing good genetic material over a wide area – distances that would not be covered naturally, at least not in a time that helps us much). Genetic Modified Organisms (GMO) food, in which we tinker with the genes directly also holds great promise but has risks, especially if we forget basic scientific principles such as biodiversity.

Voracious Worm Evolves to Eat Biotech Corn Engineered to Kill It

First planted in 1996, Bt corn quickly became hugely popular among U.S. farmers. Within a few years, populations of rootworms and corn borers, another common corn pest, had plummeted across the midwest. Yields rose and farmers reduced their use of conventional insecticides that cause more ecological damage than the Bt toxin.

By the turn of the millennium, however, scientists who study the evolution of insecticide resistance were warning of imminent problems. Any rootworm that could survive Bt exposures would have a wide-open field in which to reproduce; unless the crop was carefully managed, resistance would quickly emerge.

Key to effective management, said the scientists, were refuges set aside and planted with non-Bt corn. Within these fields, rootworms would remain susceptible to the Bt toxin. By mating with any Bt-resistant worms that chanced to evolve in neighboring fields, they’d prevent resistance from building up in the gene pool.

But the scientists’ own recommendations — an advisory panel convened in 2002 by the EPA suggested that a full 50 percent of each corn farmer’s fields be devoted to these non-Bt refuges — were resisted by seed companies and eventually the EPA itself, which set voluntary refuge guidelines at between 5 and 20 percent. Many farmers didn’t even follow those recommendations.

Using extremely powerful tools like GMO requires society to have much better scientific literacy among those making decisions than any societies have shown thus far. The failure of our governments to enforce sensible scientific constraints on such use of genetic engineering creates huge risks to society. It is due to this consistent failure of our government to act within sensible scientific constraints that causes me to support efforts (along with other reasons – economic understanding – the extremely poor state of patent system, risk reduction…) to resist the widespread adoption of GMO, patenting of life (including seeds and seeds produced by seeds).

Wonderful things are possible. If we grow up and show a long term track record of being guided by scientific principles when the risks of not doing so are huge then I will be more supportive of using tactics such as GMO more easily. But I don’t see us getting their anytime soon. If anything we are much less scietifically minded and guided than we were 50 years ago: even while we bask in the glorious wonders science has brought us on a daily basis.

Continue reading

Why Don’t All Ant Species Replace Queens in the Colony, Since Some Do

My response to: There are other species of ants that do replace the queen, so why did some species not do this?

Basically the method they evolved copes well with losing the queen. Out of various ways of dealing with having a dominant Queen some may lead to replacement if she dies.

There are lots of examples of method is very effective at creating lots of successful offspring but happens to be less than ideal in some situations. Natural selection is pretty amazing and awesome at creating effective genes but we certainly can look at the results sometimes and see improvements that would be useful.

Likely if losing the queen was very common a good way of dealing with that would be found (or that species would be disadvantaged and at risk). If the queen happens to evolve to being very reliable coping with her death becomes less important. If they produce lots of useful offspring but have a less than ideal method of coping with their home colony losing her it is entirely sensible to imagine that species could flourish.

I would imagine species with queens that had shorter lifespans, that invested more in the home colony, that were less effective at setting up new colonies… would be more likely to have better queen replacement strategies/results.

Related: Ants, Ants, AntsE.O. Wilson: Lord of the AntsAmazonian Ant Species is All Female, Reproduces By CloningRoyal Ant GenesHuge Ant Nest

80% of the Antibiotics in the USA are Used in Agriculture and Aquaculture

Citing an overabundance in the use of antibiotics by the agriculture and aquaculture industries that poses a threat to public health, economics professor Aidan Hollis has proposed a solution in the form of user fees on the non-human use of antibiotics.

In a newly released paper published (closed science, sadly, so no link provide), Hollis and co-author Ziana Ahmed state that in the United States 80% of the antibiotics in the country are consumed in agriculture and aquaculture for the purpose of increasing food production.

This flood of antibiotics released into the environment – sprayed on fruit trees and fed to the likes of livestock, poultry and salmon, among other uses – has led bacteria to evolve, Hollis writes. Mounting evidence cited in the journal shows resistant pathogens are emerging in the wake of this veritable flood of antibiotics – resulting in an increase in bacteria that is immune to available treatments.

If the problem is left unchecked, this will create a health crisis on a global scale, Hollis says.

Hollis suggest that the predicament could be greatly alleviated by imposing a user fee on the non-human uses of antibiotics, similar to the way in which logging companies pay stumpage fees and oil companies pay royalties.

“Modern medicine relies on antibiotics to kill off bacterial infections,” explains Hollis. “This is incredibly important. Without effective antibiotics, any surgery – even minor ones – will become extremely risky. Cancer therapies, similarly, are dependent on the availability of effective antimicrobials. Ordinary infections will kill otherwise healthy people.”

Bacteria that can effectively resist antibiotics will thrive, Hollis adds, reproducing rapidly and spreading in various ways.

“It’s not just the food we eat,” he says. “Bacteria is spread in the environment; it might wind up on a doorknob. You walk away with the bacteria on you and you share it with the next person you come into contact with. If you become infected with resistant bacteria, antibiotics won’t provide any relief.”

While the vast majority of antibiotic use has gone towards increasing productivity in agriculture, Hollis asserts that most of these applications are of “low value.”

“It’s about increasing the efficiency of food so you can reduce the amount of grain you feed the cattle,” says Hollis. “It’s about giving antibiotics to baby chicks because it reduces the likelihood that they’re going to get sick when you cram them together in unsanitary conditions.

“These methods are obviously profitable to the farmers, but that doesn’t mean it’s generating a huge benefit. In fact, the profitability is usually quite marginal.

“The real value of antibiotics is saving people from dying. Everything else is trivial.”

While banning the use of antibiotics in food production is challenging, establishing a user fee makes good sense, according to Hollis.

Such a practice would deter the low-value use of antibiotics, with higher costs encouraging farmers to improve their animal management methods and to adopt better substitutes for the drugs, such as vaccinations.

Hollis also suggests that an international treaty could ideally be imposed. “Resistant bacteria do not respect national borders,” he says. He adds that such a treaty might have a fair chance of attaining international compliance, as governments tend to be motivated by revenue collection.

Hollis notes that in the USA, a move has been made to control the non-human use of antibiotics, with the FDA recently seeking voluntary limits on the use of antibiotics for animal growth promotion on farms.

Related: Raising Food Without AntibioticsOur Dangerous Antibiotic Practices Carry Great RisksWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibiotics Too Often Prescribed for Sinus Woes

Mechanical Gears Found in Jumping Insects

A natural example of a functioning gear mechanism has been discovered in a common insect – the plant-hopper Issus – showing that evolution developed interlocking cogs long before we did.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box. Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

The gear teeth on the opposing hind-legs lock together like those in a car gear-box, ensuring almost complete synchronicity in leg movement – the legs always move within 30 ‘microseconds’ of each other, with one microsecond equal to a millionth of a second.

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” – causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force – then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to can create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent. It is amazing what evolution results in, not only gears but a system that changes to a different solution (maybe, who knows the real “reason”) when the gears solution lack of robustness would create a problem for survivability.

While there are examples of apparently ornamental cogs in the animal kingdom – such as on the shell of the cog wheel turtle or the back of the wheel bug – gears with a functional role either remain elusive or have been rendered defunct by evolution.

Related: Using Bacteria to Power Microscopic MachinesWebcast of a T-cell Killing a Cancerous CellBuilding A Better Bed Bug Trap Using Bean Leaves

In the video above, Professor Malcolm Burrows talks about finding the bugs that led to the science, and working with artists Elizabeth Hobbs and Emily Tracy and members of the community in the London borough of Hackney to produce the film ‘Waterfolk’.

Full press release

Learn About Biology Online

Very cool site for learning about biology. I have tried the courses offered by Coursera but they are too structured for my taste. I want to be able to learn at my pace and dip into the areas I find interesting. Coursera is more like a real course, that has weekly assignments and the like.

Survivebio [site is offline, here a site you might be interested in – iBiology] is a resources that matches my desires exactly. You can go and learn about whatever topics you desire, when you desire. The site offers webcasts, games, flashcards, chapter outlines, practice tests and a forum to discuss the ideas.

In this webcast, Paul Andersen discusses the specifics of phylogenetics. The evolutionary relationships of organisms are discovered through both morphological and molecular data.

The aim of the SurviveBio web site is to aid AP (and college) biology students. But it is also a great resource to learn about biology if you are interested in that topic. Hopefully they will add more webcasts. The site uses webcasts from Bozeman Science which has a huge number of very good videos on biology and also, chemistry, physics, earth science, statistics, anatomy and physiology.

Related: Great Webcast Explaining the Digestive SystemsCell Aging and Limits Due to TelomeresHuman Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic