DNA

My Ancestry

aardvarchaeology — Sat, 11 Mar 2017 13:20:50 +0000

My Ancestry

Inspired by Karin Bojs's and Peter Sjölund's recent book Svenskarna och deras fäder, I've looked into my ancestry by means both genetic and genealogical. Here's a few highlights.

Like most Stockholmers, I'm of mixed rural Swedish stock. My great grandpa's generation contains 16 people born mainly in the 1880s. Only one of them was born in Stockholm. His parents were born in Värmland and Södermanland provinces. The other 15 were born all over rural southern Sweden: Bohuslän (two people), Småland (two people), Södermanland, Skåne and Närke. They went to Stockholm to find work, met and got married.
My Y chromosome is type R1b-M269, which is the second-most common one in Sweden and the most common one in Western Europe. My closest modern matches form dense clusters in England and New England. There's clearly an Englishman in my recent pedigree, most likely in the 15th or 16th centuries judging from a combination of genetic statistics and genealogy. In the mid-1600s my paternal line was already in Värmland with Swedish names.
My mitochondrial DNA is the very common type H with my closest modern matches clustering in Finland. This means that my maternal line points east to a very great grandma in West Asia about 25,000 years ago. Of Europe's three original major population components, this would represent the Ancient North Eurasians.
I found the first Rundkvist! In the 1800s a lot of rural Swedes quit using the patronymic and took family names instead. My grandpa's grandpa Johan Jansson (1853-1925) took the name Rundkvist and moved to Stockholm from Fryksdalen in Värmland. His brother Magnus Jansson instead chose Söderqvist for some reason.
Update 14 March: Aard regular Lassi pointed out something enlightening. Parts of modern Sweden saw state-sponsored immigration from Finland in the decades around 1600. This is the simplest explanation for why I have a Finnish maternal line. Its earliest member known to me, Helena Helgesdotter, was born near Gothenburg in 1775.

aardvarchaeology Sat, 03/11/2017 - 08:20

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History

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sweden

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History

One of these days I should get my mother to write down a bunch of family history that she has told me and/or my sister. My mother is the last surviving member of her generation, mostly because she was the youngest (several of her cousins were a couple of decades or so older than she; she was the youngest of seven children, born to a 38 year old mother).

Some of my father's cousins are still alive, including one who lives about an hour drive from me (coincidentally; my father's side of the family lived mostly in northeastern Colorado, about 3000 km west of where I live now).

Record an interview with her about the family! I've been wondering idly about the first Rundkvist for decades, and now it turns out that I used to meet his daughter once or twice a year when I was a kid. Much family lore was lost because we never thought to record what she knew.

Useful resource, but it carries the risk of being drowned in a flood of information:
http://www.eupedia.com/genetics/

On uniparental DNA, beware sample bias in the sample of genomes tested by whichever service you used. It can be misleading. Autosomal DNA, which makes up by far the most part of your total genome, is a better bet to get a read on your total ancestry composition. If indeed you had a British ancestor, it should show up in your total ancestry composition as distinct from Scandinavian, although if it was that far back and only one individual, it will be a small % of the total. Full genome sampling and testing costs more, of course, but just uniparental is not too informative, except for general interest.

I've done Y chromosome and mitochondrial typing. Now I'm waiting for the general SNP scan that Family Tree DNA calls "Family Finder".

I have just read the book "Germans" which clears up a lot of misconceptions about the peoples with that particular language group.
BTW are there any particular genetic markers that are more common for the group that would later be known as "celts" ?

-- -- -- -- -- -- -- -- --
John, regarding the difficulty of interesting people in reading up on facts.

In my experience, it helps to start with a simplified summary in the first one or two paragraphs, because 99% of readers will just skim through the text.

So if you -for instance- are publishing a cure for cancer, readers will ignore it unless the first paragraph reads WE HAVE A FUCKING CURE FOR CANCER. It is no point being subtle when confronted with stressed-out readers.

And, yes, I know that some discoveries are so inherently complex that it is hard to boil them down to a one-paragraph summary up front. that is why it is so rare to find good science jounalists, it is a bit of a black art.

And in regard to ancestry, here are a lot of "legacy systems" for chat systems https://xkcd.com/1810/

We could be related :-)

In the 17th century the King of Sweden promised tax breaks to anyone who moved to various uninhabited parts of the kingdom. From Savonia in eastern Finland some people went to Karelia (both were parts of Sweden at the time) and become my ancestors, others moved to Värmland. Maybe your maternal Finnish ancestor was one of them.

BTW, Finnish was spoken in Värmland up to 1950s. They even sung poems that were parts of the Kalevala cycle.

Maybe some day I'll have my DNA analysed...

Excellent point, Lassi. The slash-and-burn Finns are of course the easiest way to explain why my Finnish mitochondria are near Gothenburg in 1775.

Them Romans were harder to kill than modern humans.

Gladiator 2: Maximus Overdrive https://www.theguardian.com/film/2017/mar/14/ridley-scott-gladiator-2-f…

We could be related

Go back 40 generations--about a thousand years. In theory you should have 2^40 ancestors in that generation, which is a bit over a trillion. That's 3-4 orders of magnitude more people than were alive in the world at the time, so obviously there is considerable duplication in your family tree. And given that some of my ancestors were Swedish, it's likely that I share some of those ancestors.

I remember when it was big news that Ronald Reagan and Francois Mitterand had a common ancestor in the 9th century...

Martin@4 - That's it - the 'general SNP scan' will give you the autosomal DNA, which they should interpret for you in terms of ancestry in relation to various reference populations.

When you get that, if you can, you should download your own raw data file, if indeed they don't give that to you automatically. After all, they are your data, and there are other interesting things you can do with them, using kosher software that is freely available (like medical information, if indeed you want that - my own experience with that is that the medical information is mostly not too helpful because they only sample about 2,400 SNPS. Typing a full genome is still way too expensive for most customers of consumer genomics).

Birger@5 - re. Celts, no, not unique individual uniparental markers (Y DNA and mtDNA). Remember me babbling a while back about the 'great homogenisation'? They have to use autosomal DNA and compare with reference populations, using statistics. The Celts are not recognised as a distinct identifiable culture until the Iron Age; the great homogenisation was over some time during the Bronze Age.

I'm assume I'm not babbling to a bunch of average punters here - at least you, Martin and Eric have fully functional brains (plus I am keen to see the intersection and synthesis of genetic and archaeological information - most linguists seem just not interested), and I presume (perhaps wrongly) that you have at least some prior relevant knowledge. I have no interest in trying to enlighten the general readership here, let along anywhere else. When I try to talk to intelligent friends who have not taken any interest in developments in modern genetics, their eyes just glaze over.

Birger@4 - Further to my verbose babbling above, to try to clarify - please appreciate that it is difficult to be succinct about a branch of science that has absolutely exploded since the 1990s, but about which most people seem to lack even a fairly fundamental understanding, so let me start by using this as a hook: CELTS WERE NOT FUCKING UNIQUE. In fact, I have read that they were a culture, rather than a 'race', which is probably as good a way to put it as any.

The most dominant Y DNA (i.e. male line) haplogroup in Western Europe is R1b (but only second most dominant in Sweden). Martin belongs to R1b - M269, which is the most common haplogroup subgroup in Western Europe. I belong to R1b - L21. Among ancient remains identified archaeologically as 'Celtic', R1b is highly represented, as it is in all European groups dating to the Iron Age.

That includes the Basques, who are notable for speaking a non-Indo-European language. People were misled by that for a long time and thought that the Basques must be a remnant of some very old population in Europe, but they are not - somehow, the Basque language remained intact, but the population changed with time to look like pretty much most other populations in Western Europe. The stand-out group among Western European populations are the Sardinians, who lack the Ancient North Eurasian component which is present in all other European populations to some extent, thought due to geographic isolation during the period around the end of the Neolithic/beginning of the Bronze Age when pastoralists from the Pontic-Caspian steppe entered Europe in a wave of migrations. But, just to be contrary and confuse everyone, although the Sardinians are genetically distinctive and lacking ANE ancestry, they speak an Indo-European language, the language group that is associated with the steppe migrations, which are also associated with a substantial component of ANE ancestry.

So, Genetics 101 - languages do not map particularly well to populations in terms of genetics, as the Basques and Sardinians demonstrate. The Celts had a distinctive material culture and languages, but they are not notably distinctive genetically - certainly not like the Sardinians.

Ötzi the Iceman matches most closely to Sardinians, i.e. he had no Ancient North Eurasian ancestry, which places him among the Neolithic wave of migration into Europe from the Near East. He had among the possessions he carried a copper-headed axe, which is yet further confirmation that at least some Neolithic groups in Europe had copper, before the migrations of the steppe peoples.

Ancient remains identified archaeologically as Celtic cannot be identified as such by a unique set of genetic markers, just as the Basques cannot be. They can only be identified genetically by the relative composition of the group as a whole. Of course, the remains of an ancient Celtic individual can be identified wrt to Y DNA, and that male line can be tracked down to modern times. Apparently 12% of modern Irishmen can trace their male lineage to someone called Niall of the Nine Hostages, whoever the fuck he was (I have no idea, and no wish to find out), to the extent that it has become something of a joke on the Internet discussion boards - if you're Irish, the genomics companies will tell you that you are descended from this Geezer, along with seemingly everyone else in Ireland.

In the British Isles and Ireland, on a population basis, modern Irish, Scots and English cannot be differentiated (much to the chagrin of some people). However, if a single person is genotyped, then by reference to ancient population groups, that individual's ancestry can be broken down so that he can be identified as so many % Anglo-Saxon, so many % Celtic, so many % Danish, etc. because reference population sets have been established for those ancient groups, now that enough ancient remains have been genotyped who are identifiable by archaeology, e.g. associated with grave goods or whatever. So, people in East Anglia have a relatively high proportion of Anglo-Saxon ancestry; people in the north of England might have a higher proportion of Danish ancestry, people in the far south of England who might have a higher proportion of Celtic, etc. But none of them is 'pure', they are all mixtures.

So, the typical English geezer who proudly pronounces that he is 'descended from a Viking' is just being a delusional dick telling self-aggrandising stories in the pub to anyone not too bored to listen - on a whole genome basis, he is no doubt just plain white modern English bread like everyone else. My favourite story is from a Singaporean Chinese woman I know who lived in England for a while - when people used to start that sort of one-upmanship in the pub, she used to say "I'm descended from a shipping clerk and a bus conductor." In fact, her personal ancestry is actually more interesting than most of them - her ancestors come from Hainan Island, which is a whole other long-winded subject.

It's complicated. If you sample from the Eurogenes Blog, run by the Polish blogger who calls himself Davidski, you will quickly see just how complex the whole field has become.

Lassi@7 - Go for it. Endless hours of fun.

When Martin gets his ancestry composition it will predictably set him off on another journey of discovery, depending what his results show; especially, of course, if he comes out as something less than, say, 95% Scandinavian. I have some revealed ancestry for which I have absolutely no explanation at all - it is totally absent from the family genealogical myths that I was told by all of the older relatives who are now dead. They would have been as mystified as I am.

My wife finally opted to spit into a sample tube a month ago, so we are waiting to get her results. She is getting impatient to know. My anticipation is tempered by the knowledge that the American company we used does not have a really good reference population for East Asians, aside from Asian Americans, who are dominated by Southern Han (they have sampled over one million individuals, but their total sample is overwhelmed by Irish and North Americans of Irish ancestry, who all seem to be mad keen genealogists). But of course they have access to the global GWAS database, like all of the genomics companies. So their analysis of ancestry is improving all the time. Research on the origins of East Asians has lagged badly, as has genomic research in Africa, but it is now in the process of catching up.

The basic message I have been trying to push on this Blog for some time is that all of this delving into ancient genomes from the remains of anatomically modern humans in Europe NEEDS THE FUCKING ARCHAEOLOGY TO ANCHOR IT. The two disciplines are complementary and potentially mutually enlightening and confirmatory. Actually three, if the linguists were willing to engage, but most of them appear not to be - they seem to fear that their discipline will be 'contaminated' if they allow it to be informed by these other disciplines. I suspect they are just pissed off that it is the geneticists and archaeologists who together have settled the question of where the Proto-Indo-European Urheimat was, while they have argued endlessly and fruitlessly about it among themselves. Those linguists who ignore the mass of evidence now available are the ones who seem to continue to get it wrong.

If you think this is not a succinct attempt at a summary, try reading Davidski some time. There is no short cut for stressed readers into the field of modern genomics, any more than there is any short cut into the field of, say, Scandinavian archaeology - you need to read the stuff, even at the popular science level.

Celts "were a culture, rather than a ‘race’".

An archaeological culture is a list of types of object and structure that occur reliably together: all material stuff. The Hallstatt and La Tène archaeological cultures were probably largely associated with Celtic languages.

But we're pretty sure that there were groups who spoke other languages yet used variants of the material culture. And conversely, not every single Celtic-speaking group is likely to have used the material culture. Further, we know from social anthropology that tribal societies like these encourage multilingualism. Are you a Celt if Etruscan is spoken regularly in your household?

So the only really undisputed way to use the word "Celtic" is in reference to language. Which does not survive much from the period in question.

I was thinking Anglo-centrically, where people totally conflate Celtic material culture, languages and genetic populations (and notably art among the New Age crowd), which I think they can just about get away with (please correct me if I'm wrong).

I don't even want to think about 'Celtic' material culture and languages in Europe - that just gets far too confusing for me, having being taught in an Anglo-centric tradition from a very young age that Celts were an identifiable population grouping who spoke an identifiable group of languages.

Yeah, in the British Isles there is to my knowledge no sign of any pre-Celtic language stratum, so that's what people spoke there until the Roman invasion.

There's a recent school of thought that argues that the language group originated along the Atlantic coasts of Europe and then expanded east into Central Europe, rather than the reverse which is the established idea.

But if there were a pre-Celtic language in the British Isles, how would we know? Neither group had writing at the time, so if the invaders thoroughly defeated the previous indigenous group, the latter group may not have left any trace.

Of course one clue might be geographical names. In the US and Canada, many rivers, lakes, and even cities and states/provinces have indigenous names. Likewise in Japan, as you go northeast you are increasingly likely to encounter geographical names which are of non-Japanese origin (presumably derived from the ancestral language of the Ainu). It helps to have some kind of gradient or abrupt transition so that you can identify this situation.

In the case of the Celts, this signal is further attenuated by the subsequent Anglo-Saxon and Viking invasions of the British Isles. Certainly the Celtic influence in place names is visible: multiple rivers named Avon, which was an indigenous word for river, and the possibly apocryphal Torpenhow Hill ("Hill-hill-hill Hill").

For many of the indigenous peoples of North America, particularly in the eastern part of the continent, place names are the only trace of the indigenous language. Contemporary accounts by European settlers note cases where as much as 90% of the indigenous population died in disease outbreaks. In some cases enough native speakers remained to keep the language alive despite the efforts to force children to attend "Indian schools" where they were forced to use only English. At least two, Cherokee and Inuit, acquired their own writing systems (the former is obsolete, but you may see the latter in parts of Arctic Canada), though most of the remaining indigenous American languages have adapted the Latin alphabet to their languages, similar to how Portuguese missionaries created a Latin-derived alphabet for Vietnamese.

Birger@5: Still trying to find a rational response to your question, you can refer to Eupedia here: http://www.eupedia.com/europe/celtic_trivia.shtml

To quote: "Genetic studies determined that most of the ancient Celtic men belonged to the Y-DNA haplogroup R1b-S116 and its subclades. Two Early Bronze Age migrations brought the L21 subclade to north-west France and the British Isles, and the DF27 subclade to south-west France and Iberia. The third major Celtic subclade is S28 (aka U152), which is associated with the expansion of the Hallstatt and La Tène Celts, as well as with Italic tribes."

But the writer(s) don't explain how they identified those 'ancient Celtic men' as being Celtic, or what they mean by Celtic, and they don't identify where the 'two early Bronze Age migrations' came from - maybe we can infer from the steppe, given that Celtic languages were Indo-European languages; they appear to conflate material culture with language, and it all pretty much dissolves into hyperbole after that.

No, that was a ridiculous thing to say - they can't have been steppe migrations.

If the Atlantic coast theory is right, they would be coming from the other direction, anyway.

I assume 'they' (whoever they are) are assigning 'Celtic' to these subclades based on an association with material culture, which is interpreted to be 'same' as Hallstata and La Tène. But as 'Celtic' refers to a language group, at least in modern parlance, that's dodgy.

It hasn't escaped my eagle eye that they include the R1b-L21 subclade in this, which is my own. Well, north-west France could work.

We also know that the Celts didn't call themselves that. As I understand it, the term is derived from the Greek κελτο&iota (keltoi), which means "barbarian". Which implies that at the time there were Celtic people living in what is now the Balkans.

There is a portion of northwest France called Brittany. It was one of the last places in continental Europe where Celtic languages were spoken, along with Galicia in northwest Spain.

Using Feces to Identify Species

dr. dolittle — Wed, 28 Sep 2016 10:37:22 +0000

Using Feces to Identify Species

Image of big eared bats By Stihler Craig, U.S. Fish and Wildlife Service [Public domain], via Wikimedia Commons

According to a press release from Northern Arizona University, Drs. Faith Walker and Carol Chambers at the Bat Ecology & Genetics Lab have developed a system called Species From Feces to identify bat species from guano collected in field locations such as mines, caves, bridges, etc. The system takes advantage of DNA sequencing technology and an assay to look for genetic identifiers unique to different species using DNA barcodes. The sequences can then be compared to a searchable database to identify what species of bats were present at that location.

This method is a great way to screen populations for endangered species and to verify what species of bats have been in a location. The team reports that their technology has been used to differentiate species that look similar as well.

dr. dolittle Wed, 09/28/2016 - 06:37

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Extreme Physiology: Radiation tolerance

dr. dolittle — Wed, 21 Sep 2016 16:55:26 +0000

Extreme Physiology: Radiation tolerance

Don't let their small size fool you. Tardigrades, or 'water bears', are really tough animals. According to a review published in the American Scientist, these microscopic invertebrates can survive extreme variations in temperature from near absolute zero (-459 deg F) up to +302 deg F. They can also tolerate pressures that are 6 times greater than the deepest ocean, exposure to ionizing radiation (UV and x-ray) and the vacuum of space, as well as exposure to carbon dioxide and monoxide, nitrogen and sulfur dioxide. What's more, they can survive nearly complete dehydration, an ability called anhydrobiosis. To survive these extreme challenges, the animals go through a state called cryptobiosis during which time they shut down metabolism until the threat is over. For animals that live in moist environments with periodic dry spells, dehydration is a threat.

A new study published in Nature Communications examined whether water bear cellular tolerance to dehydration and radiation could be transferred to human cells. The researchers suspected that because both these threats damage DNA, water bears may use the same protein to protect their tissues. The team sequenced the genome of a species of water bear (Ramazzottius varieornatus), then inserted portions of the genome into cultured human cells. Just as they had suspected, they discovered a gene called Dsup that can prevent DNA damage caused by exposure of the cells to x-rays as well as dehydration.

The hope is that this discovery may lead to therapies to help protect people receiving radiation therapy or those who work with radiation. It may also help in the development of crops that can tolerate extreme temperatures or radiation - farming on Mars anyone?

Given their amazing tolerance to extreme environments, I am sure the water bear genome sequence will lead to additional discoveries of protective proteins.

Sources:

Nature

American Scientist

Video By Halberg K, J?rgensen A, M?bjerg N [CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

dr. dolittle Wed, 09/21/2016 - 12:55

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New site, new stories

jhalper — Sun, 03 Jan 2016 05:05:53 +0000

New site, new stories

Cells that “spit” out their contents and messenger RNA that is not so swift at delivering its message. Those are two brand new stories on our new and improved website. Check it out and let us know what you think.

The first story arose from a simple question: How do secretory cells – those that produce copious amounts of such substances as tears, saliva or all those bodily fluids – manage to get their contents out of the cell? Cells are walled all the way around; they don’t really have doors for letting things the size of a drop of fluid out. Instead, they use the vesicle system – small globes made of the same stuff as the cell membrane that transport the drops out to the edge. The vesicles then fuse with the membrane, releasing their cargo to the outside.

Prof. Ben-Zion Shilo and his group realized that this was all well and fine for small amounts of biochemicals, but secretory cells would need a better system. Their results, which involved a lot of intricate time-lapse observation in the saliva glands of fruit-fly larvae, are beautiful to watch as well as instructive.

Salivary gland of a larval fruit fly. Vesicles (red) carrying the glue must empty their contents quickly and efficiently

The second story arose from a surprising observation: Certain liver cells that are involved in metabolism seemed to have large amounts of messenger RNA in their nuclei. Why would RNA stick around in the cell nucleus, instead of rushing out to make proteins? Dr. Shalev Itzkovitz and his group followed up on this question by asking further questions: How many cells keep RNA in their nuclei? How long does this RNA tend to stay? Which genes produce the homebody RNA?

Although they have not yet answered every one of their questions, they have uncovered a new level of regulation in the cell – one that is not immediately intuitive.

Nuclei of liver cells, mRNA of certain genes in white

Revealing how some cells get rid of their contents or discovering that others hoard things deep within – neither finding will cure disease tomorrow. Both are changing our understanding of how the human cell functions, and both are going to contribute, in the future, to human health and welfare. We promise to keep bringing you these stories and more.

jhalper Sun, 01/03/2016 - 00:05

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biochemistry

biological regulation

biological regulation

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Books On Fossils and Evolution

gregladen — Wed, 25 Nov 2015 11:20:17 +0000

Books On Fossils and Evolution

Over the last several months, a lot of great books on fossils and evolution (as in paleontology) have come out. I've selected the best for your consideration. These are great gifts for your favorite science-loving nephew, life science teaching cousin, or local school library. Actually, you might like some of these yourself.

Let's start off with a kid's book: Grandmother Fish: a child's first book of Evolution by Jonathan Tweet.

From the blurb:

Grandmother Fish is the first book to teach evolution to preschoolers. While listening to the story, the child mimics the motions and sounds of our ancestors, such as wiggling like a fish or hooting like an ape. Like magic, evolution becomes fun, accessible, and personal. Grandmother Fish will be a full-size (10 x 8), full-color, 32-page, hardback book full of appealing animal illustrations, perfect for your bookshelf. US publishers consider evolution to be too “hot” a topic for children, but with your help we can make this book happen ourselves.

I reviewed the book here before it first came out. This was a kickstarter project, and it may be currently unavailable commercially, but if you click through to the kickstarter project you can probably get a copy of it.

The most recent book to come across my desk is Don Prothero's The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution. I've got a review of Prothero's book in my draft file, so look for that post coming out over the next few days.

One might ask, "how do you choose 25 fossils, among so many choices, to represent evolution?" Well, Don cheated a little by mentioning more than 25 fossils. Also, you really can't do this. Don selected fossils using several criteria, but one basis for his choice was the availability of rich historical information about a fossil's discovery, interpretation, and effect on our thinking about evolution. And, he covers all of that.

Don is one of those rare authors who is both an expert scientist and a great writer, with a proven ability to explain things in a way that is not watered down yet totally accessible.

Here's a selection of the many other books written by Prothero:

Evolution: The Whole Story is an astonishing book that needs to be on the bookshelf of anyone interested in evolution. The work is edied by Steve Parker, but authored by nearly a dozen experts in various subfields of fossils and evolution, so it is authoritative and scholarly. At the same time, it is very accessible and enjoyable. This is not a book you read from cover to cover, though you could. Feel free to skip around, and you;ll find yourself looking stuff up all the time.

The book is divided into major sections, and each section has a series of short pieces on this or that fossil, group of fossils, type of life system, method for studying fossils, etc. There is a running sidebar on the bottom of many pages giving "key events" in evolutionary history of the group of life forms under consideration The book is VERY richly illustrated, with detailed keys to the illustrations. Many of the illustrations are broken down into "focal points" that expand significantly on the illustrations' details. There are countless additional inserts with more information. The book itself is beautiful, intriguingly organized, and it is full of ... well, everything. The book is very well indexed and sourced, and has helpful, up to date, phylogenies and chronological graphics.

The Biology Book: From the Origin of Life to Epigenetics, 250 Milestones in the History of Biology (Sterling Milestones) by Michael Gerald and Gloria Gerald is a compendium of biological topics and key moments in the history of biological science, organized in a sort of chronological framework. Major groups (the insects, the amphibians), major ideas (Pliny's Natural History, Ongogeny and Phylogeny), key physiological and developmental concepts (meiosis, mitosis, many topics in endocrinology), key fossils (like the Coelocanth) and so on are discussed, very nicely illustrated. This is almost like having a gazillian short articles from Natural History Magazine (or similar) all in one book. There are 250 biological "milestones" in all. The charming part of the book is that a milestone can be an evolutionary event, an extinction episode, the emergence of a great idea, or a particular discover. And, as noted, these are ordered across time, as well as one can, from the beginning of life to a selection of the most recent discovery. The book effectively combines history of biology (and related sciences) and the biological history itself.

Life's Greatest Secret: The Race to Crack the Genetic Code by the well respected scientist and historian Matthew Cobb is a carefully and clearly written history of the discovery of the nature of DNA, covering a lot more than, and since, Watson and Crick. It is extremely well sourced, indexed, and supported, and very readable.

This is the detailed and authoritative work on all the elements that came together to understand the genetic code. Don't talk about the discovery and understanding of DNA any more until you've read this book. From the publisher:

Life’s Greatest Secret mixes remarkable insights, theoretical dead-ends, and ingenious experiments with the swift pace of a thriller. From New York to Paris, Cambridge, Massachusetts, to Cambridge, England, and London to Moscow, the greatest discovery of twentieth-century biology was truly a global feat. Biologist and historian of science Matthew Cobb gives the full and rich account of the cooperation and competition between the eccentric characters—mathematicians, physicists, information theorists, and biologists—who contributed to this revolutionary new science. And, while every new discovery was a leap forward for science, Cobb shows how every new answer inevitably led to new questions that were at least as difficult to answer: just ask anyone who had hoped that the successful completion of the Human Genome Project was going to truly yield the book of life, or that a better understanding of epigenetics or “junk DNA” was going to be the final piece of the puzzle. But the setbacks and unexpected discoveries are what make the science exciting, and it is Matthew Cobb’s telling that makes them worth reading. This is a riveting story of humans exploring what it is that makes us human and how the world works, and it is essential reading for anyone who’d like to explore those questions for themselves.

Extinction and Evolution: What Fossils Reveal About the History of Life is a an updated version of a classic book about evolution and extinction written by one of the scientists who developed our modern way of thinking about evolution and extinction (especially the extinction part).

Eldredge's groundbreaking work is now accepted as the definitive statement of how life as we know it evolved on Earth. This book chronicles how Eldredge made his discoveries and traces the history of life through the lenses of paleontology, geology, ecology, anthropology, biology, genetics, zoology, mammalogy, herpetology, entomology and botany. While rigorously accurate, the text is accessible, engaging and free of jargon.

Honorable Mentions: Older books that are great and may now be avaialable for much reduced prices.

I really liked The Great Transition: Shifting from Fossil Fuels to Solar and Wind Energy as an expose of a particular time period and major event in geological history. Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet by Prothero is a classic, again, looking at a fairly narrowly defined moment in prehistory. You can get it used for about five bucks.

The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution by Dean Falk is a great book focusing on one key human fossil. This is a personal story as well as a scientific one. Again, available used for a song.

Have you read Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body yet? I'm sure you've heard about it. It is still a great read, and you can get it used cheap.

The only book I would recommend that uses the "paleolithic" to advise you on diet and exercise is The Paleolithic Prescription: A Program of Diet and Exercise and a Design for Living.

gregladen Wed, 11/25/2015 - 06:20

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A systematic approach to melanoma mutations

jhalper — Tue, 27 Oct 2015 05:46:17 +0000

A systematic approach to melanoma mutations

Metastatic melanoma tumors. Left exhibits low or absent expression of RASA2 and reduced survival, typical of about 35% of patients. The sample on the right exhibits high RASA2 expression and increased survival

Rates of melanoma are increasing, even as the rates of other common cancers are decreasing. According to the Melanoma Research Alliance, it is the most common cancer diagnosis in young adults 25-29 years old in the United States, the second most common cancer in young people 15-29, and its incidence has tripled in the last 30 years.

What are we doing about it? The Weizmann Institute’s Prof. Yardena Samuels has a database of over 500 samples from melanoma patients, and she is using this information to figure out how mutations drive the cancer. This is easier said than done. The damage to our DNA from the sun’s radiation can be widespread – a single melanoma cell can have hundreds of mutations.

Samuels and her group are going about the process systematically: They looked within a particular subset of melanomas – a group that often has a poor prognosis – for a particular type of gene. The genes known as tumor-suppressors are often mutated or inactivated in cancer. When they work, they protect us from cancer by keeping the brakes on cell growth or telling a cell with cancerous mutations to commit suicide. When they don’t, they not only fail to prevent cancer from growing and spreading, they can be rooked into aiding the process.

The melanoma tumor-suppressor Samuels and her group found interacts with an oncogene that is common to the set of melanomas they were looking at – apparently regulating its activities.

How does one restore the function of a gene that is lost or mutated? That is the question that the group is now addressing. “Now that we have identified the tumor suppressor, we can work out its pathway in the cell and understand how it is meant to function. And that, we hope, may lead to some ideas for treating this subset of melanomas – up to 35 percent of the cases. Among other things, this work highlights the need for more personalized diagnoses and treatment protocols for cancers like melanoma,” says Samuels.

Prof. Yardena Samuels (front left, in white) and her group. Drs. Rand Arafeh and Nouar Qutob (standing to the right and left of Samuels, respectively) led the study

Also online today:

A link between the immune system and obesity: when certain rare immune cells are missing, mice gain weight, even on a regular diet.

A brake on plants' starch production machinery that turns it off at night -- but stays lightly depressed during the day too.

jhalper Tue, 10/27/2015 - 01:46

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basic research

Biological networks

biological regulation

personalized medicine

biological regulation

genes

Genetic Modification as Medicine

milhayser — Wed, 03 Jun 2015 12:14:38 +0000

Genetic Modification as Medicine

On ERV, Abbie Smith provides an update on a pioneering treatment for hemophilia that uses viruses to insert missing genes in a patient's DNA. Hemophilia results from from the mutation or deletion of a gene that makes a blood clotting agent called Factor IX; without it, hemophiliacs are at risk for uncontrolled bleeding. While Factor IX can be delivered pharmaceutically, utilizing viruses to modify patients' DNA yields long-term improvements in natural Factor IX production. Abbie writes, "the amount of therapeutic Factor IX these patients needed (on average) dropped from 2613 IU/kg to 206. The people who got the ‘high’ dose of virus dropped that down to 92 IU/kg. They went from 15-16 ‘bleeding episodes’ a year, to one." They also saved $2.5 million.

Next, Abbie revisits research on treating HIV by removing CCR5 receptors that the virus uses to enter white blood cells. Much excitement was generated in 2008 when the "Berlin Patient" was declared to be functionally cured of HIV after receiving bone marrow from a donor with a mutation that preludes manufacture of the CCR5 protein. Now scientists are considering using gene therapy to disable CCR5 production in HIV patients, but there's a catch: some HIV quasispecies utilize other receptor proteins, and even a small population of such viruses can take over when a patient is not producing CCR5. For this reason, Abbie writes that this therapy may hold more promise as a vaccine for HIV than as a cure.

Meanwhile, HIV itself has been genetically modified to help some sufferers of acute lymphoblastic leukemia by training cytotoxic T cells to target cancerous B cells. Abbie writes, "for all the time HIV has stolen from people, from families, its nice to see it giving some time back."

milhayser Wed, 06/03/2015 - 08:14

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Misc

Acute Lymphoblastic Leukemia

A bacterium's sense of self explained

jhalper — Mon, 27 Apr 2015 03:52:55 +0000

A bacterium's sense of self explained

Foreigner or native-born? Your immune system discriminates between them, as do those of bacteria. Yes indeed, bacteria do have immune systems – pretty complex ones at that. And like any useful immune system, the bacterial ones must have a good technique for distinguishing “foreign” from “self.”

You may even have heard of the bacterial immune system: It’s called CRISPR, and it’s used in biology research around the world for DNA engineering and genome editing. CRISPR normally inserts short DNA sequences taken from phages – viruses that invade bacteria – into special slots called spacers within its genome. These bits of DNA form an “immune memory” – the record of past infection that helps fight the next one. The phage sequences are used as a template to create “antisense” RNA-protein complexes that can identify and take out further phages that try to sneak into the cell. This kind of immunity is adaptive and, until recently, scientists did not think that bacteria had something so sophisticated as an adaptive immune system.

bacteria cell and phages. Wikimedia commons

Within less than a decade of its discovery, researchers had revealed how CRISPR works and even found how to use it for other purposes, but there were still some fairly big open questions -- especially how it discriminates between foreign and self. How can it look at two sequences of DNA and know that one belongs to a phage, the other to its own genome? For a bacterium, this is quite critical: Mistakenly inserting a bit of self-DNA could cause a fatal “autoimmune” attack. But if the cell misidentifies the phage DNA as self, the results could be no less deadly. And the ID system must be nimble, as well, since most environments are home to many more phages than bacteria.

Prof. Rotem Sorek and his group, working with researchers at Tel Aviv University, “infected” bacterial cells with round bits of DNA called plasmids and then recorded some 38 million separate immunization events to see how and where the selection occurs. (That’s no mistake: They really have data from 38 million events.)

The CRISPR foreign-self discrimination mechanisms they discovered astonish and delight because they are clever and efficient, and they use the bacteria’s DNA copying machinery to do the job. Extra DNA stuck in the genome – say from a virus that wants to get replicated – will gum up the machinery as the DNA double strand is being unwound in preparation for copying. A stall in the process brings in the repair enzyme; this enzyme, along with several CRISPR-associated proteins, checks out the sequence.

In the end, it all comes down to differences in replication: Viral DNA, which pretty much exists to reproduce, will have a lot of genetic bits that replicate at high rates. What it won’t have much of is another sequence that is found all over that bacterial genome, which tells the copying machinery to stop. So if the repair machinery finds lots of one and doesn’t run into the other, it can “assume” the DNA comes from a phage.

Why should we care about a bacterial immune mechanism? In truth, many think we need to start taking more of an “ecosystem” approach to the whole subject of bacteria and viruses – our world is teeming with them. So, for example, if we want to use phages, as some have suggested, as antibiotics, we might have to understand how the bacteria could develop resistance. On the other hand, some of the first to investigate the commercial use of CRISPR have been the yogurt producers, who can lose their bacterial cultures to phages. Phages can also live symbiotically inside bacteria, and in the case of certain hosts, cause harmless bacteria to become pathogenic. And, of course, phages are part of your personal ecosystem – present in and alongside the microbiota that live in your gut and on your skin.

Sorek is now looking for other bacterial immune systems – CRISPR is found in only around half of all bacteria, so there are sure to be others. And that, he says, will open up a whole new set of questions about discrimination on the microscopic scale.

jhalper Sun, 04/26/2015 - 23:52

Whose DNA is that?

dr. dolittle — Thu, 12 Feb 2015 23:09:23 +0000

Whose DNA is that?

Official New York City Subway Map

Dr. Christopher Mason (Weill Cornell Medical College, Manhatten, NY) decided to sequence DNA found in NY subway stations...468 of them to be precise. At each station, his research team collected DNA samples by swabbing the kiosks, turnstiles, benches, railings, trash cans as well as the subway cars.

Along with finding abundant Pseudomonas bacteria (also found on our skin) they discovered that the DNA at each of the stations reflected the amazing diversity of the local residents and what they were eating such as pizza, cucumbers, and chickpeas, which may simply be components of more complex foods. They also discovered fragments of DNA from anthrax and plague, although they said, "We have zero evidence that they're alive or remotely pose a risk to public health." In fact, they discovered around 1700 different organisms. What was interesting is that about half of the DNA discovered could not be traced back to any of the gene sequences for organisms that have been identified thus far. Don't take this the wrong way, it doesn't mean that we have aliens riding in the subways. Instead it points out that there are many organisms out there for which we have yet to sequence their DNA.

According to a quote from Dr. Mason in Scientific American: "And the study has replaced what used to be sort of a fog of almost fear maybe about what might be on the surface to concrete knowledge that the vast majority of everything under our fingerprints is mostly benign, so, I've become much more confident."

You can listen to a podcast of the story here

Sources:

E Afshinnekoo, C Meydan, S Chowdhury, D Jaroudi, C Boyer, N Bernstein, JM Maritz, D Reeves, J Gandara, S Chhangawala, S Ahsanuddin, A Simmons, T Nessel, B Sundaresh, E Pereira, E Jorgensen, S-O Kolokotronis, N Kirchberger, I Garcia, D Gandara, S Dhanraj, T Nawrin, Y Saletore, N Alexander, P Vijay, EM He'naff, P Zumbo, M Walsh, GD O’Mullan, S Tighe, JT Dudley, A Dunaif, S Ennis, E O’Halloran, TR Magalhaes, B Boone, AL Jones, TR Muth, KS Paolantonio, E Alter, EE Schadt, J Garbarino, RJ Prill, JM Carlton, S Levy, CE Mason. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Systems. 1:1-15, 2015.

Scientific American

dr. dolittle Thu, 02/12/2015 - 18:09

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This sounds like interesting stuff. By the DNA not being traceable to the DNA sequence records does it mean that maybe they evolved from other microbes or simply just erupted from the surface of the earth ?

During the research experiment how were all the DNA samples distinguished from one another because I assume there would be thousands of DNA samples on top one another in a publick place such as a subway ? How do the mixture of DNA samples not alter the accuracy of one another if they form layers on one another. U14017769
U14017769

How are the traces that were found of anthrax and other diseases not harmful to humans, seeing that anthrax can cause great devastation? Is it just due to the fact that they are only in small amounts?
u15010130

Is it difficult to see what proteins the DNA has a code for? Because to trace it all the way back to the assimilating proteins of a 'pizza' sounds a bit complex. u15169988

If there are roughly 8500 organisms we cannot account for, whose DNA we cannot sequence as of yet, how are we sure that there is no harm within them and that they cannot cause any damage to us? Are we still with certainty able to classify them as benign?

Chance Cancer Mutations

milhayser — Mon, 26 Jan 2015 14:08:12 +0000

Chance Cancer Mutations

This new year, researchers concluded that 2/3 of the difference in cancer risk between different parts of the body can be attributed to the number of stem cell divisions those parts undergo. More cell divisions reflect a higher risk as errors that occur naturally during the DNA replication process can contribute to the development of cancer. In other words, the same genetic mutability that enables evolution also ensures that many people will be afflicted by a terrible disease. On Pharyngula, PZ Myers suggests this is one reason our cells naturally get old and stop dividing: because if they continued forever, too many mutations would accumulate in the individual.

Of course, mutations are rare and unpredictably distributed, and not all of them are dangerous, making who gets cancer largely a matter of chance. The new study shows which cancers are most influenced by lifestyle factors such as using tobacco. PZ writes,"colorectal and lung cancers do have a significant risk beyond what can be accounted for by stochastic errors, so pursuing a reduction in exposure to risk factors, like diet and smoking, can have a useful role in reducing the incidence of these cancers." On the flip side, the incidence of pancreatic cancer (for example) can be totally accounted for by random mutation.

milhayser Mon, 01/26/2015 - 09:08

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