Genesis: The Scientific Quest for Life's Origin

For book club this month we chose a book titled Genesis: The scientific Quest for Life's Origin by Dr. Robert Hazen

The topic of the book is a discussion of the current theories of how life may have emerged from the non-living chemical rich primordial earth. The word for this transitional event is autogenesis.

I've read a lot about evolution, but I was really interested to learn more about the beginning of life, specifically its creation. What does it even mean to be alive? It's easy to clarify in terms of humans, and mammals, but when you get down to smaller, simpler things, the answer becomes fuzzy. How did the first life form on earth organize itself? And how do scientists even begin to answer that question a few billion years later?

These were all questions I had going into this book, and I have to say that for the most part my curiosity concerning them has been satisfied. That's not to say the book had complete and definitive answers to my questions, but rather that it addressed them, and gave the best possible answer (as it is understood by scientists today), or answers if there were more than one possibility. It was both an overview and a history of the subject, and for the most part an easy read. The only difficulty was when the author explained certain chemical reactions, and used names like isoprene and phenathrene etc. But they were necessary to document in that they supply the "proof" to the claims the scientists are making concerning the origins of life and ultimately ourselves.

I wrote in the previous blog about emergent systems. Well, this seems to be the prevailing theory on how life on Earth came about. Through an unique combination of chemicals and the right influx of energy, life was able to emerge. I find that utterly fascinating. It was also really interesting to me how large a role geologists are playing attempting to answers to the origin of life questions. By examining rocks and the chemical signatures entombed within them they are helping biologists and chemist find clues to how life evolved. If I ever go for my PhD, I think this is where I'd focus.

The book begins by exploring a few of the many ways that life can be defined. From philosophical, religious, and scientific views come all kinds of answers. But the one that was used as a “working definition” by the author came from Dr. Gerald Joyce a member of a NASA exobiology panel. He said; “Life is a self-sustained chemical system capable of undergoing Darwinian evolution”.  And that works for me. It’s not very romantic sounding, but it gets the job done.

The book also recounts the history of some of the earliest origin-of-life experiments, back in the 1950’s. Among them the most famous Urey-Miller experiments where an early Earth atmosphere was simulated using ammonia, methane and hydrogen. When they sparked the mixture (as a proxy for lightning strikes) they were able to produce many amino acids, which are the building blocks of life! Those experiments, while inaccurate (the composition of the early atmosphere has been refined in recent years) created a lot of interest and basically began modern hunt for the origin of life.

The book also discusses the possibility of life elsewhere in the universe, spending a lot of time to examine the evidences for and against life on Mars through the inspection of the famous Allen Hill’s meteorite, or ALH84001.

The book discusses the methods of teasing out information from rocks millions of years old, and explains in pretty extensive detail the current experiments that are being conducted and what they hope to tell us about the origin of organic life.

There were really interesting chapters on chemosynthetic life (i.e. life that gets its energy from chemical reactions rather than the sun) and discusses microbes living miles beneath the Earth’s crust in in tiny pockets of otherwise dense rock.

There was a chapter about the possible mechanisms that evolved RNA (the precursor to DNA) that led to more complex life.

There was a discussion about how clay particles might have been the template for DNA, and how minerals could have substituted for membranes before primitive cells knew how to make their own!

There was so much unique information that I feel bad not covering it all in this review, but to go into any more depth would require a lot more explaining on my part, and I think in that case you’d probably be best off just reading the book yourself.

Anyway, in closing, I give this book four out of 5 stars. It was well written, easy to read (for the most part), extremely interesting, and I think it covered the subject thoroughly and in depth enough to be educational without being too technical. It also provided a history of how we got to where we are now, and a window into the future research on this mind boggling subject.

ATTENTION: If you are super lazy or don't like reading, but want to learn more about this I found a talk on the book given by the author on YouTube! You can check it out HERE.

Emergence

Termite mound: Example of an emergence system.
(borrowed from getintravel.com)

The book I read for book club this month touched on something called emergence. And because it's so interesting to me I thought instead of trying to incorporate it into my book review I'd write a separate blog about.
Emergence has come up briefly in a couple other books I've read recently, and I'm pretty fascinated by it at the moment.(Like I was with strange attractors a couple years ago;) But what is it? To borrow the definition from Wikipedia emergence is:
"...the way complex systems and patters arise out of a multiplicity of relatively simple reactions."
What this means is that in many systems patterns will begin to emerge that could not be predicted beforehand by looking at any single component of the whole system. Saying it another way, emergence is the production of a pattern or a complex systems by many individual components that could never create anything on their own. Moreover, the system cannot work unless all of the components are in place. It's slightly more complicated than just that, since to create emergent properties a specific amount of energy must be added to the system, but I'll try to explain that below. This is a really cool thing, so I'm going to take a minute to give a couple examples.
Sand ripples: If you look at the components that form sand ripples in the bottom of a lake or ocean you have: Water, wave action (i.e. your energy source), and sand grains. If you  look closely at a sand grain, or a molecule of water, it is unlikely that you could predict how they could ever organize themselves into coherent rows of ripples. But they do. The thing is, they only do it when the right amount of energy (i.e. waves) are present. Too little energy and they will not form. Too much (think big crashing storm waves) and the ripples will be destroyed. But just the right amount, and suddenly sand grains can organize themselves into ripple patterns. Cool right?
Termite nests: This works for hives as well. The components to these systems are earth and millions of individual insects. The energy to the system is how much work each individual can do. Now if you took a single termite and inspected it closely you'd never guess that it could build a mound twenty feet tall. It doesn't even know how to "build"! And you'd be right, a single termite can't build a mound. Even several hundred couldn't, but a few million can, and do. A bunch of individually simple termites can build gigantic mounds taller than a giraffe!
The human brain: Same thing. Your components are individual neurons, and of course the energy comes from the food you eat. If you look at a single neuron you can see how it basically works, but it can't create complex thought...or even simple thought for that matter. All it can do is send and receive chemical signals. You can't make a "sort of brain" with a few hundred neurons. You need a whole skull full of them, all connected together, to be able to think, and learn and know. A brain is not a neuron, a brain is an intricately connected assemblage of many neurons that when acting together produce thoughts and regulate body functions.
So why is this important and interesting to me? This subject of emergence is critical for the transition from non-living to living. The primary reason being that it explains how the evolution of life was able to occur and not conflict with the second law of thermodynamics (i.e.entropy of a system never decreases). To be clear, technically nothing gets around the second law, so ultimately everything does increase in entropy. But small isolated systems like termite mounds, or shallow shore lines, or human brains, can under the right circumstances, for a time, produce amazing and complex things. Using only specific quantities of energy, and relatively simple parts amazing patterns and functions quite literally emerge! I think that is so cool.
Anyway, I'm probably not explaining this super well, but it's my hope that if you find this subject interesting, you will look it up and do some reading on your own! I am sure there are authors out there who have done a much better job than me. On is Dr. Robert Hazen who wrote the book Genesis: The Scientific Quest for Life's Origin that I read for book club this month.

We are our Synapses

One of the many books I have read lately is Synaptic Self by Joseph LeDoux. It's one of the most interesting books I've ever read about the subject of who we are. For those of us who don't believe in things like souls or spirits, the questions surrounding who we are have been difficult to answer. Of course the solution lies somewhere within the mushy folds of the brain, but where and how does it all come together to make me feel like myself?
Well, this book answers that question. And in my opinion the author does it clearly and methodically. It was simply a fascinating read. He begins simply, and sort of teaches you as you go about the different functions of brain regions, the interaction of chemicals and the processes that influence them. He interweaves the history of neuroscience with our modern understanding of how the brain works. His discussion on depression and anxiety were really interesting, as well as his explanations of how medications are taken up and used by the body.
It took me forever to read (on and off for a couple months), but I never lost interest, and I enjoyed it every step of the way. It was definitely not an easy read. In fact thinking back on it, it was more like the summary of a textbook and less like pop-science.

Stem cell neurons.

It is truly amazing how brains work. It seems nothing short of a miracle, yet it is made up of normal things, it functions using the laws and relationships that nature has provided everything else, and it was created by a universe that can't even know itself like the thing it created. Truly one of the most awesome things I have ever thought about. And to think I have a whole brain (at least I think it's a whole one), right up in my head, to keep all for myself, and use for all of my life! Sweet.

I recommend this book to anyone interested in a biological understanding of who we are. 5 out of 5 stars on this one.

The Origin of AIDS

As a change from the physics kick my book club has been on the last few months we read a book about virology, biology, and the history of disease. The Origin of AIDS by Jacques Pepin, was an...I don't want to say "awesome" (because it is truly tragic)...but a brilliant book. I love a book that has more references than it does text!
Pepin chronicles the history, not only of the disease but of the research, the forensic investigation into the origin, and propagation of the deadliest disease to touch the modern world. He sleuthed out the truth buried in mounds of reports and papers published in the early to mid-20th century, and in long forgotten blood specimens hidden in freezers in central Africa. He presented data, clearly and fairly, and he warned against interpreting data that you don't understand (which was an excellent point!).
I thought the book was not only insightful in terms of the obvious topic, but also a fantastic example of the use of the scientific method, and an informative history of Africa during the era of colonialism.
Contrary to what many Americans might think, HIV and AIDS didn't originate within the homosexual community, but rather it was a disease acquired from chimpanzees, and initially transmitted through the unsterilized needles of colonial doctors trying to control (then) known diseases like African sleeping sickness, yaws, syphilis, malaria and leprosy. Only then did it spread to prostitutes and then later to Haiti where it finally encountered the US homosexual community. The story is a sad one, and tragic in the true sense of the word, but it was also encouraging in that science has been able to understand HIV and AIDS to the extent that has, and in such a short time. Only 20 years ago AIDS was considered an un-curable death sentence. But (and unfortunately this only applied to non-3rd world countries) now it is something that can be controlled and people can live long relatively healthy lives. Just look at Magic Johnson. He was diagnosed in 1991 I think.
Technically the book was profound too. It got scientific, but not in a gratingly boring kind of way. I'll admit that there was much more information than I really needed, but at the same time, in some cases I really appreciated it. For example I didn't know that the primate version of HIV is called SIV, and there are many variations within the chimp/gorilla/monkey populations around the world. I didn't know that because SIV has been around in primates for a couple thousand years, most of them are immune to it now (the ones that weren't died off long ago and never reproduced). Hopefully the story of HIV and humans will eventually play out in the same manner. I didn't know there was an HIV-1 and HIV-2. I didn't know that HIV-1 had subtypes, the most common being HIV-1 M, but additionally there is an N, O, and P each indicating a different cross-species transmission from ape (or monkey) to human. That fact was especially amazing to me for some reason. There was just tons and tons of fascinating information like that throughout the book.
Like I said before, at the same time that the story was tragic, it was also inspiring. The contrast between the devastating topic, and the medical genius that finally discovered it's MO, was a little difficult to navigate emotionally at times, but it was absolutely worthwhile read.
I definitely recommend it, not only as an interesting scientific topic, but also as a wonderful example of the use of the scientific method, and a piece of recent history. It's a piece of history we still are a part of, and I think it is worth while to try to understand it.

The Birds and the Bees...Literally.

Chapter 2 in The X in Sex

I mentioned in an earlier post that I was reading a book called "The X in Sex". Well, I finished it. And I know I say this about almost every book I read (and it's true!) but this was so interesting! Plus it was well written, and even funny in parts....I mean who can't appreciate a chapter entitled "The Duke of Kent's Testicles?" It's even more amazing to me because the subject of the book (minus the portions about testicles of course) is actively, at this very moment, doing all the things that I am reading about...inside every cell in my body. It's weird feeling to learn about my insides, and understand myself in such a way. I mean, there are processes going on in my body right now that...even with the aid of a book, I'll probably never understand. But somehow it's still me. How could I not know myself?!? Ha ha...It's just so weird...and awesome. I love it.

I learned so many cool things from this book that I am afraid if I try to cram them all into one blog it will be...sort of long and unfocused. So instead I am going to try to break it down into a few segments.

But before we start talking about the familiar males and females, X and Y and all of that, I thought it might be worth while to go into a little more depth on the multiple ways a living thing can create progeny. Bear with me if it seems a little redundant to the last post about this book. I'm going to try to be a little more specific.

Sex happens to be the one us mammals and many reptiles and birds use, but it is by no means the only (or even most efficient) way to produce offspring. And some of them are pretty incredible, at least as strange as our own way. As most of you probably know reproduction is broadly divided into sexual and asexual.
Asexual can be broken down into parthenogenisis, binary fission, budding, fragmentation and many other, but more obscure methods.
Fission and budding are mostly accomplished by bacteria, some viruses, and plants, and while they are interesting in their own right (and have many advantages), I'd much rather focus on parthenogenic species, because they are just so neat. They are animals that can reproduce without a male (or an opposite sex). Primarily they are mother/daughter species (although some can produce males once in a while, or be all male species) where the genetic material from the mother is passed directly and completely to the daughters. The classic pathenogenic species are aphids. But science has now discovered that some bees, lizards, hammer head sharks, Komodo dragons, and boa constrictors also reproduce this way!
When we move onto sexual reproduction things might become more familiar because there are boys and girls, but the methods of producing the XX/XY or ZZ/ZW (in birds and reptiles) can be totally foreign still! Besides our "normal" way of reproducing there are hermaphrodite species, like snails and many amphibians that can have both male and female sex organs at the same time (and fertilize their own eggs) or have the ability to change from male to female during their life cycle. Some species of frogs, when the ratio of male to female gets disrupted, can convert many of it's population to the less dominant sex to balance things back out again!
Or there is what is called "external fertilization" in contrast to our internal method. Salmon do this. A female will lay her eggs in the water, and a male will come by later and fertilize the eggs, and all the mating happens outside the body of the female.
Even when we finally get to talking about sexual reproduction where there are distinct males and females and the females are internally inseminated by males, the process can be wildly unfamiliar.
Humans (and all mammals) use genes to determine sex. XX and you have a girl XY and it's a boy. But there are many sexual species (with males and females) who don't use genes to determine sex! What do I mean? Well, here are two examples.
Bonellia is a kind of worm that lives in the ocean. They have males and females, but it is not genes that determine the sex of the offspring, rather it is the environment. The female creates sexless larvae that float around in the ocean. Eventually they drop to the ocean floor, and it is here that they decide what sex they will become. If the larvae falls and there are no other Bonillia around then it will become a female and root. If the larvae falls and there are other Bonillia around then it becomes a male, burrows into the side of the larger female, and essentially becomes a symbiotic...testicle! (Angler fish, as I mentioned before, also have a symbiotic relationship with each other.)
A second example is that of the Nile Crocodiles.They don't use genes or environment to determine sex, they use temperature! The sex of the baby crocks is determined by the temperature of the eggs during the middle of the third incubation period. If the temperature is above 34.5 degrees C or below 31.7 degrees C then the offspring will be female. But if the temperature falls within that 4 degree window, the babies will be male!

Often times we view the natural world with the idea that it is somehow perfectly designed, that there is an methodical simplicity in it, but I disagree. Especially when it comes to reproduction.  It seems to me life will try anything and everything. Males/females, females/females, males/males, male-females, males-then-females, non-sexed to sexed, non-sexual, clones, spores...etc. It reminds me of the game Boggle, where you use a discrete number of  letters to make up as many words as you can. So life has done with reproduction. Using the building blocks available, life tried every combination it seems,without bias. And the ones we are left with are the ones that worked better than the other possible combinations that are no longer with us.
Our human sexual reproductive ways have many advantages (primarily genetic diversity) and it is truly amazing how our bodies reproduce, but our strategy is far from perfect, and far from being the only way to get things done. And there are many weird, dramatic, and often unfortunate concequences embedded in our chosen methods. I will begin to discuss those in the next post.
But the take away point here is that there are pros and cons to every method of reproduction. None is perfect, none is flawless, and most of them are not even ideal. But the one thing they have in common (and the only thing they need to be viable forms of reproduction) is that they do in fact create survivors. You and I are one of them, and so is every other living thing on earth. Groovy. Yay for reproduction!

X Chromosomes

Most of the time when I go to the library I am looking for a specific book. But once in a while I like to just peruse the shelves and see what catches my eye. I found a book all about the X chromosome in this way. It is called The X in Sex. I spent an hour or so reading it by the pool yesterday and it's pretty interesting stuff. As most of us know XX makes a girl and XY makes a boy. But the how of that is slightly more complicated...and it turns out its quite different (and pretty complicated)  for the two sexes. And they why of why we have two sexes (and not three or one) is also pretty interesting too.
Unlike the story of Adam and Eve, the human body is actually by default a woman. (It should have been Adam formed from Eve's rib and not the other way around.) That is, the body was designed to be a woman's, but with the substitution of the second X for Y it can be modified into a man's. The creation of a male is a more active process with genes coding for inhibiting certain processes and the alteration of the existing body plan, where creation of a female is more about just letting what is trying to happen, happen. Of course we are talking about mammals here.
One chapter of the book was on all the other forms of reproduction, some of which are truly bizarre. Some animals can change their sex half way through their lives, in some animals the ambient temperature surrounding the future offspring can determine it's sex, some animals have both sets of sex organs and can impregnate themselves! Aphids don't have males...just mothers and daughters, and in some marine species, males attach to a female body and loose all individuality (eyes, internal organs) and actually become a growth on the female, s a....sperm satchel. See the Angler fish below. (The only thing worse than being a sperm sack, is being a sperm sack attached to an female angler fish...ugggg gnarly.)
Anyway, I'm only half way through the book but it is really interesting. I'll write another post if I find any more noteworthy stuff!

Angler female and male

Save the Manatee

I read a short article in the November/December issue of Sierra Magazine about how the U.S. Department of Fish and Wildlife was proposing to make Kings Bay, Florida into a manatee refuge. The manatee's overwinter there, and last year two of them were killed by boaters. This tragedy is even worse because manatee's are an endangered species, and "vulnerable to extinction".
Apparently though there is  a group called the Citrus County Tea Party Patriots who oppose this proposition saying "We cannot elevate nature above people. That is against the Bible and the Bill of Rights."
And while I know I must be careful not to stereotype all religious people, I would like to point this out as maybe a more extreme example of why I don't believe science and religion will ever be compatible.
First of all saying that people are not a part of nature is...frankly wrong. If you don't even understand basic fact then...well, there probably isn't much point in even trying to explain anything else. The fact that as far as "life" is concerned we are equal with slime molds, flying squirrels and chimpanzee's makes us a part of nature. The fact that our bodies obey the same laws of physics as the solar system, and the Milky Way makes us a part of the universe. When we destroy life, we destroy ourselves. When we discover something new about the universe, we discover something new about ourselves. To truly respect, and understand science you can't think of yourself as something separate from it.
Now, I understand that religious folks believe they are divinely created, but even if that were true, does that then give them the right to treat other life (especially ones that can't protect themselves) like crap? I mean do these Tea Party Patriots really believe allowing a bunch of drunk rednecks to race around in speed boats, and water ski is better than saving a species that is endangered because of us? Do they really believe that humans have the right to be fascist dictators over the rest of nature? WTF?
I'm not even going to touch the "against the Bible and Bill of Rights" thing. It's so stupid an argument it's not worth the energy or time.
I'm not saying all religious people are like this, but I'm saying there are some, and they are usually the loudest. And they are hurting science, and all of us with their ignorant ideas. And I for one don't have the patience for it.

Power, Sex, Suicide

So this months book for book club was called Power, Sex and Suicide, by Nick Lane. Despite the fact that it sounds like a cliche romance novel, it's topic was actually mitochondria, and everything you ever did (and did not) want to know about them.
I have to say it was a fascinating book, and totally worth the time I spent trudging through the technical biology review that comprised the first few chapters.
Biology is so....freaking amazing. And the way all of it fits together and works and reproduces is almost hard to believe. I feel like saying it's perfect, and in a philosophical sense I guess I do mean that. But from a technical standpoint biology is not perfect, it's only as good as it has to be to get by and produce progeny. And maybe that's better than being perfect:)
Anyway I thought I'd share a couple "higlights" from the book with you all.
The first is that the author believes that the evolution of life is (on a cosmic scale) inevitable, and that there are probably bacteria-like lifeforms all over the place. He also thinks that things like sight, flight, multicellular life, are also "not improbable". He believes if life were to be wiped out on earth, it would rise again given enough time. But he firmly and adimantly believes that the evolution of eukaryotes (Cells with nuclei and a cell membrane) was a very rare and unlikely result of life on earth because of the way in which it most likely came into being. The difficulty he argues is not producing life itself, but producing eukaryotes. I thought that was interesting because I'd always thought if we ventually found life on Mars, and it was some kind of bacteria, then it would say a lot about the possibility of intellegent life elsewhere in the universe. But Lane argues that may not be the case. It might be extreemly common for bacteria to inhabit every nook and cranny of every habitable planet, but that doesn't necessarily imply that complex life is common or even probable elsewhere.
The second thing is that most scientists believe that mitochondria were once independednt bacteria that somehow eventually became incorporated into already existing eukaryotic cells, but the author asserts that it's too hard to explain how the cell worked before the introduction of mitochondria (which produces all the energy in the form of ATP for cellular function), and therefore argues that the eukaryotic cell evolved simultaneously with mitochondria, and that....bit of luck as it were, is his reason for why it is so much harder to imagine complex life sprouting up everywhere.
The third thing I will mention is that the author also thinks the reason we age and die is not because our telomeres become shorter (as was or is? the reigning hypothesys) it's because of the free radicals produced by mitochondria as they produce ATP. As you age, copies of cells, and the mitochondria within them become less faithful in their construction, and as those errors accumulate in new mitochondria they produce more and more free radicalsand not only destroy the mitochondria themselves, but also the protiens within the cell that perform all kinds of vital functions. They also loose their ability to alert the cell that something is wrong and when it's time to die. Contrary to what people think (like all those people taking tons of anti-oxidants and all that crap) you actually need some amount of free radicals in your body because they regulate overall cell health. It's a no win situation in a way. The free radicals age you, but you can't live without them.
Maybe someday biomedical technology will find a way to change out your mitochondria every ten or twenty years, and we will all live to be several hundred! Wouldn't that be somthing?
Fourth thing is that we have so many mitochondria (which except in VERY rare cases we ONLY inherit from our mothers) that they make up 10% of our body weight!
And finally just because I thought this was kind of funny, and totally explained why I cannot be a vegetarian or eat vegan meat substitutes I thought I'd toss this in. We all have methanogens (methane producing bacteria) living in our guts. We also have sulpher eating bacteria in there competing for space (its a bacterial war zone!) Anyway the methane producing little guys prefer to abide inside vegitarians becase veggies contain little sulphur and so there aren't as many sulphur loving bacteria to compete with. They tend to take over the place and as they enjoy their private party they make you more farty. LOL.
Anyway, there was a lot more in the book, and actually a bunch of really interesting things about bacteria that I didn't know. But I think I'll save that for another day. If you have ever had an interest in learning about mitochondria I highly recommend this book!

The painting is by me of what else? Mitochondria!

Meet My DNA

I know I've already written several posts today, but you are going to have to humor me with one more. I'd post it tomorrow, but it's so exciting I just can't wait.
It's weird how much of ourselves we've never seen. I'm not talking about that freckle on you left shoulder blade, I'm talking about your brain or heart for example, or a white blood cell or your DNA. In the case of the latter, sure we've heard about it, and we know basically what it is, and we know that we have millions of copies in our bodies, but have you ever actually seen DNA, in "the flesh" so to speak?
Well, I have! And not just any old DNA either, I've actually seen my DNA! I extracted it just a half hour ago, and right in my own kitchen as a matter of fact! It only took the simplest tools and method, and surprisingly it is the same procedure (more or less) that professionals use. Isn't that something?
With nothing more than some salt water, soap, a little alcohol and a few drops of spit, I was able to collect, unwind and view my very own DNA! *sigh* Ain't science grand?
Here are a few pictures of one of the better "strands" that I saw. They are really small, and so quite difficult to photograph. I had to use a combination of hand lens at 10x magnification, and my awesome camera, and even so it is still a little tough to make out. (It wasn't as difficult in real life.) But basically my DNA is the thing that looks like a little piece of string suspended in the liquid inside the circle of the lens. I also have a picture of the entire jar over a light, where you can see much more DNA, but it didn't unwind as well, so it looks like little white specks.  Enjoy!

Who's Your Great-Great-Grand-Daddy?

The other day at the gym I was surprised to see an issue of the journal Science among the normal fitness/body building ones in a basket in the lobby. I was a little early for yoga, so I sat down for a quick read. As I thumbed through some of the shorter articles I came across one discussing the recently-complicated family tree of we humans that was pretty neat.
For the past 100,000 years or so we have been tooling around the earth doing our "thing" which involved learning, creating culture, reproducing and all that fun stuff. But many of us forget (or maybe never realized to begin with) that we weren't the only folks around at that time. In the past 35,000 years there were Neandertals for one, and archaic humans called the Denisova hominin in addition to ourselves. And if you go back to the beginning of that 100,00 years when Homo sapiens emerged there were probably a few of our older ancestors still running around, like Australopithecus sediba and so on.
Anyway, for almost the entire history of anthropology it was thought that we humans never mated with any of our  early neighbors. But DNA sequencing is turning that idea on it's head. Recent study comparing modern human DNA to Neandertal and Denisovan DNA has produced the following results:

• Eastern Europeans and Asian people have inherited 2%-6% of their DNA from Neadertals.
• Peoples of Southwest Asia have inherited about 5% of their DNA from the Denisovans, and another 4-6% from Neandertals. (Another study found this same distribution in people in the Philippines, Southeast Asia, and Melanesia.) (That's about 10% total!!!)
• Denisovan DNA was found in Australian aboriginals
• Three isolated African groups inherited DNA from an unknown archaic people, long after modern humans arose.
• It has been discovered that over half of the human genes that code for leukocyte antigen proteins, (i.e.the ones that help detect pathogens in the blood) came from some or another "archaic" human.

I guess maybe I should point out before closing what is meant by archaic humans. They were still Homo but their DNA shows them to be distinct from us modern humans. They appear to have evolved from the same ancestors as Neandertals, but were closely enough related to humans to be able to reproduce.

Note: You may notice that I spell Neandertal with a "t" rather than a "th". I believe the "th" is the American version, but in all of my readings (both in school, and in scientific journals) always uses the "t" version, and I figured if it's good enough for Science it's good enough for me.

You have Beautiful...Eye.

Water flea
http://discovermagazine.com/2012/mar/30-heres-looking-at-you-kid

I saw this photo in the most recent edition of Discover Magazine at the local library, and then I searched it out on their website (which by the was is fantastic,and totally one of my favorite Internet haunts). The image is of a water flea. Yep. Can you believe that? I sat there for at least five minutes trying to figure out if it was some kind of joke or something, but it's not. It's the real deal. And I think this little guy/gal...whatever, is pretty awesome (and I'm invoking the original sense of the word here, not the modern day meaning). The article is short, but definitely worth the one minute it will take to read it. The other highlight the author points out is that these transparent little specks have about 5,000 more genes than we do! I don't know how that's possible, but there you have it. I swear that every single day I am more amazed by what life is, and how life does. It reminds me of that quote by the late Carl Sagan. "I find it elevating and exhilarating to discover that we live in a Universe which permits the evolution of molecular machines as intricate and subtle as we." Although just for today I might replace the "we" with "a water flea".

On a slightly more humorous note for some reason the water flea photo instantly reminded me of this seedy plankton character that I saw on Sponge Bob. I looked it up and his name is Sheldon J. Plankton...LOL...

The second thing I thought of was Mike Wazowski. 

Paedophryne amauensis

Paedophryne amauensis is the smallest (and I might add the cutest) frog in the world...at least that we know of. Don't you just love nature. Just when you think you've seen it all, something new and unexpected appears! Just look at this little guy! I mean he makes a dime look spacious!

The Blind Watchmaker

We just read The Blind Watchmaker by Richard Dawkins in book club this week. Well, actually we had all month to read it and then we discussed it last night at our January meeting.
I can't say it was my favorite evolution  book ever, but it had some really good points, especially for "beginners" who don't have a lot of background in evolutionary biology. The thing that made it a little less than great for me was that it was so thorough. Normally that's a good thing (and for those with no previous knowledge on the subject it is a good thing) but for me he got very...long winded in parts and so I found it to be a less than easy read.
But I do recommend it for anyone who has ever wondered how evolutionists explain the complexity of the human eye, that is so often cited by Creationists as proof that god must exist. It's basically a discussion of the difference between single step (which is what most Creationists believe evolution to be based on) and cumulative selection, which is the way it actually works.
There is also a really interesting chapter on how bats use sonar to see. It turns out it is a pretty complicated process on account of the fact that the noise they make is so loud (to them) that it would burst their ear drums so they have developed a way to close their ears when they chirp, and then open them quickly to pick up the returning sound. They can do this up to 100 times per second. There is a bunch more to it, but that was the gist of it. Super cool.
So if you are interested, REALLY interested in understanding why you don't need to invoke the supernatural to to create the human eye, or explain life on earth, than I highly recommend this book. He doesn't cut any corners, and explains pretty much everything right down to the last atom. I found a free pdf of the book online and you can too if you do a search for The Blind Watchmaker pdf in Google.

Glowing Kittens

Glowing Kittens! (image from discovermagazine.com)

        Well, it was only a matter of time before scientists "made" kittens that glow as well as puppies. These adorable little guys are being used to study feline HIV (which apparently can also infect monkeys). The virus was inserted into the eggs of the mother to see whether the kittens would be immune to feline HIV afterward. In order to tell if the virus actually made the transfer it was tagged (i.e. inserted into the virus) with a bioluminescent gene from jellyfish that would glow under a black light. The 'glow' was used to confirm that the virus indeed made it into the kittens, which is obviously a necessary control on the experiment. Isn't that ingenious? Oh science, you've done it again!

Question of the Day

I was having a conversation with my BF the other day, and I was trying to explain to him how life evolves which eventually transformed into us reciting quotes from the Ben Stiller movie Meet the Parents...anyway somewhere in our discussion this question was raised:

Why do men have nipples?

I must confess, I have no idea. It doesn't fit with anything I know about the evolution of humans. Did men once lactate?  Or are all men sprung from women, and so retained the characteristic? I haven't done any research on it, maybe I will this weekend. But before we find out, do any of you want to theorize with me on possible answers?

Evolutionary Psychology

One of the many books I have been concurrently reading is called The Moral Animal by Robert Wright. And I have to say that out of all the books I've read recently, this one is by far the best. And by the best I mean that my mind is blown every few pages. I've spent a couple hours actually reading it, and several days contemplating the implications the author asserts. I'm only half way done, but it's so compelling that I thought I'd write about the subject now, and maybe post some thoughts about the content again later.
The book is a summary of the history of, and current research being conducted, in the rather adolescent field of evolutionary psychology.
This new branch of science is, in and of itself, a fascinating concept. Where psychology is the study of human thought and emotion, evolutionary psychology is the inquiry into why we have thoughts and feelings in the first place, and how hundreds of thousands of years of evolution has shaped our interpretation of a moral self.
The biggest insight to me has been the kinds of questions that evolutionary psychology asks. It addresses questions that most of us have probably never even considered. For example. Pornography (I just finished reading the section on this so I'll use it as an example since it's freshest in my mind). Everyone knows it's more of a "guy" thing than a girl thing. (I'm not stereotyping, it's been documented.)  But evolutionary psychology asks why don't women feel the same way about it? It asks why does it take an entire romance novel to convince a woman of the same feelings that a Playboy centerfold can produce in a guy in two seconds? The end result is the same (sex) but the road to get there is totally different. It goes further to ask the question why do men  become physically...agitated by a two dimensional image of a naked woman, but not compelled into fatherhood by a similar image of a baby? Likewise a woman can see a naked man on paper and not be impressed at all, but will resort to making kissy faces at an ad for diapers with a cute baby smiling on the page (again, not stereotyping, it's documented).
Aren't those interesting questions?  I mean there has to be something to it, because you don't see pubescent boys locking themselves in their bedrooms and fantasizing about being dad's, or teenage girls aspiring to be porn stars.
It's amazing to me to realize that I've overlooked so many weird things we humans to because they are "normal" for us. But when you step back, and approach our humanity with a more critical eye, you begin to notice disparities in our actions that our own intellect can detect once properly focused. Like I said before, mind blowing!
OK, that's all for now but stay tuned for more!

Sphincter Says What?

This has been my week for learning  semi-gross, yet strangely fascinating facts about biology. So just today (yes I can be cutting edge once in a while) I read an article about sphincter cloning.
It might be hard to believe, (and to be honest I have a hard time accepting the fact that I totally believe you can  replicate butt holes but still doubt whether or not wearing white after Labor Day is acceptable ) but scientists have successfully cloned a mouse sphincter! And while I am certain going from a mouse to a human is an exponential process (literally) it's a great achievement.
All poop jokes aside, (and I have a ton) it's really an amazing thing. Many people think the worst thing that can happen to you as you get older is to get wrinkles, or get grey hair. But there are much more embarrassing prospects that can occur with aging that can greatly reduce your quality of life. And the fact that there are folks out there looking to improve my prospects when I'm 70 is something that I will not take for granted. It's a modern day miracle.
Read here for the full story!

Go Ahead, Introduce Yourself

The next time your sitting in traffic and looking for something to do, instead of flipping through the radio stations or singing off key to your favorite Weezer album, it might be more fun to introduce yourself to the colony of bacteria living in you belly button. According to new research there are 1400 different species of bacteria currently eking out a living in the navels of homo sapiens around the globe. Not all 1400 are in the your belly button (at least I hope not). You probably harbor 40 to 150 independent species. But it's still pretty cool isn't it?The major determinant as to the number of "colonists" residing in your navel has less to do with personal hygiene and more to do with whether you are an "innie" or an "outie". I am pretty sure those aren't technical terms although they should be, because I for one would totally read an article in Science if the words innie, and outie were in the title followed by a a long list of authors with PhD's.
Not that anyone cares, but personally I am an "innie". I definitely get it from my dad's side of the family. Or maybe just my dad....Hmmm...
For a more factual account of Middle Waist ecosystems read here.
VIVA LOS TRES B'S!!!! (Belly Button Bacteria)

Christmas List: Item 3

Borrowed from the Associate Press

A glow in the dark PUPPY!!!!!! Yes! This is real! Isn't it adorable? This one glows red, and there is another that glows green. The set of two would would be the PERFECT addition to the holidays! Watch the video here.

(Actually, they fluoresce under a black light because some scientists in Korea replaced a protein with one that glows. RAD!)

Here Jelly, Jelly!

Lion Mane Jellyfish

Another under water behemoth I came across on my reading of The Universe Below is the Lion-Mane Jellyfish, the largest jelly in the world. And holy mackerel, is it ever! I think I'd die of shock if I ever came face to....er...um...blobby head with one of these guys. I wonder if they could eat a human? Oh my gosh! I just thought of an awesome idea! Wouldn't that be a cool alternative to being buried in a coffin, or cremated, to instead be fed to a giant jellyfish? I like it. What do you think?