Archives For evolutionary biology

brainpower

According to a widely reported paper by accomplished molecular geneticist Jerry Crabtree, the human species is getting ever less intelligent because our society removed the selective drives to nurture intelligence and get rid of mutations that can make us dumber. This is not a new idea by any means, in fact it’s been a science fiction trope for many years and had it’s own movie to remind us of the gloom and doom that awaits us if we don’t hit the books: Idiocracy. Crabtree’s addition to it revolves around some 5,000 genes he identified as playing a role in intelligence by analyzing the genetic roots of certain types of mental retardation. Then, he posits that because we tend to live in large, generally supportive communities, we don’t have to be very smart to get to a reproductive age and have plenty of offspring. Should mutations that make us duller rear their ugly heads in the next few thousand years, there’s no selective pressure to weed them out because the now dumber future humans will still be able to survive and reproduce.

Evolution does have its downsides, true, but Crabtree ignores two major issues with his idea of humanity’s evolutionary trajectory. The first is that he ignores beneficial mutations and that just two or three negative mutations won’t necessarily stunt our brains. Geneticists who reviewed his paper and decided to comment say that Crabtree’s gloom and doom just isn’t warranted by the evidence he presents, and that his statistical analysis leaves a lot to be desired. The second big issue, one that I haven’t yet seen addressed, is that Crabtree doesn’t seem to have any working definition of intelligence. These are not the days of eugenicists deluding themselves about their genetic superiority to all life on Earth and most scientifically literate people know that survival of the fittest wasn’t Darwin’s description of natural selection, but a catchphrase created by Herbert Spencer. Natural selection is the survival of the good enough in a particular environment, so we could well argue that as long as we’re smart enough to survive and reproduce, we’re fine.

This means that Crabtree’s description of us being intellectual inferiors of our ancient ancestors is at best, irrelevant and at worst pointless. However, it’s also very telling because it fits so well with the typical assessment of modern societies by eugenicists. They look at the great names in history, both scientific and creative, and wonder where our geniuses are. But they forget that we do have plenty of modern polymaths and brilliant scientists and that in Newton’s day, the typical person was illiterate and had no idea that there was such a thing as gravity or optics and really couldn’t be bothered to give less of a damn. Also, how do we define genius anyway? With an IQ test? We know those only measure certain pattern recognition and logic skills and anyone could learn how to score highly on them with enough practice. You can practice test your way to be the next Mensa member so you can talk about being in Mensa and how high your IQ scores were, which in my experience tend to be the predominant activities of Mensa members. But they are members of an organization created to guide us dullards to a better tomorrow after all…

But if IQ scores are a woefully incomplete measure of intelligence, what isn’t? Depends on who’s doing the measuring and by what metric. One of the most commonly cited factoids from those in agreement with Crabtree is how much time is being spent on Facebook an watching reality TV instead of reading the classics and inventing warp drives or whatnot. But is what we usually tend to call book smarts necessary for survival? What we consider to be trivial knowledge for children today was once considered the realm of brilliant, highly educated nobles. Wouldn’t that make us smarter than our ancestors because we’ve been able to parse the knowledge they accumulated to find the most useful and important theories and ideas, disseminate them to billions, and make things they couldn’t have even imagined in their day? How would Aristotle react to a computer? What would Hannibal think of a GPS? Would the deleterious genetic changes Crabtree sees as an unwelcome probability hamper our ability to run a society, and if so, how?

Without knowing how he views intelligence and how he measures it, all we have is an ominous warning and one that single-mindedly focuses only on potential negatives rather than entertain potential positives alongside them, and making conclusions about their impact on a somewhat nebulous concept which isn’t defined enough to support such conclusions. In fact, the jury is still out on how much intelligence is nature and how much is nurture, especially when we consider a number of failed experiments with designer babies who were supposed to be born geniuses. We can look at families of people considered to be very intelligent and note that they tend to have smart kids. But are the kids smart because their parents are smart or because they’re driven to learn by parents who greatly value academics? We don’t know, but to evolution, all that matters is that these kids secure a mate and reproduce. To look for selection’s role beyond that seems more like an exercise in confirmation bias than a scientific investigation into the origins of human intelligence. That research is much more complex and elaborate than gene counting…

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sad trex

Just in case you haven’t heard, dinosaurs were not all giant, scaly, greenish beasts. In fact, an astounding number of them had multicolored plumage like birds and share multiple specialized anatomical features with them, clearly showing that birds are descendants of these immensely popular extinct creatures. But to Ken Ham, the Australian preacher with a six figure salary drawn from his followers’ donations and millions of dollars tied up in an empire of mis-education which promotes his belief that the Flintstones wasn’t an animated Honeymooner’s rip-off but a serious documentary, these new discoveries are an affront to the Almighty. You see, since the dinosaurs were created on the fifth day about 6,000 years ago they were huge, reptilian creatures as the Bible says, so for scientists to say that it’s not actually what happened must be another atheist plot to test the faithful, or worse yet, doubt their decision to see his temple of ignorance.

So, as detailed by Brian Switek, fresh off his attempt to publicly debate with Bill Nye The Science Guy, Ham is campaigning to restore the image of the giant hulking dinosaur brute to keep the steady flow of tourists coming to Kentucky. To me, the most depressing part of this issue is that his religion marketing instinct is probably right. Bring in the kids with dinosaurs and set them up so you can hit them right between the eyes with fundamentalist propaganda and wishful thinking that eliminates all doubt and curiosity. And whenever someone points out that this is what he’s doing, he can cry about religious persecution. Why oh why won’t those evil meanies in lab coats respect his beliefs no matter how misguided, self-serving, or backward, he’ll cry with a stream of crocodile tears and pleas for donations. Switek seems to agree that this is Ham’s strategy here as well, summing up his objections in this quote…

We have an undeserved deference to faith in this country. Someone need only [to] start a sentence with “I believe…” and whatever miasma spills out of their mouths becomes beyond reproach. But our essential and cherished freedom to express our religious beliefs doesn’t mean that those same ideas should be free from criticism and even ridicule. We have let our brains slide out our skulls and through the door if we don’t question someone who claims that carnivorous dinosaurs like Allosaurus lived in the Garden of Eden and honed their teeth and talons on coconuts before the Fall of Adam brought sin, and hence death by carnivory, into the world.

Sadly his statement about beliefs is all too true. We’ve all met someone who uses the seemingly simple and innocuous phrase "well, as a person of faith" to really mean "because I’m better than you" and a license to lecture you about life, and we’re all told to respect others’ beliefs. But if we don’t draw a line and stand our ground against beliefs obviously proven false, and dismantle the faithful’s transparent attempt to ignore, dismiss, and marginalize even the most concrete of facts that proves their ideas wrong, as we saw when the windbags who run Conservapedia had the bad sense to pick a fight with a scientist who lead one of the most superb studies on evolution published in recent memory, we end up with problems like Science and Technology Committees in Congress filled with ignorant blowhards who proudly show off their aversion to facts to media outlets when discussing important policy debates and school boards which use political ideology and religion to justify throwing science books out of science class. Religious fundamentalists see this as a plus, but in reality, the country and its education and workforce suffer for it.

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Why did the state of Tennessee just let a bill allowing teachers to preach creationism in the classroom if they really felt like it without any repercussions? Well, according to writer Tom Bartlett, it’s because evolution isn’t an exciting enough story for the public while creationism has the right mix of sex, violence, and drama to vie for people’s attention. In fact, evolution isn’t even a story at all, he continues, citing a professor of psychology’s conclusion that evolution’s lack of a protagonist, motivation, or determined outcome disqualifies it as what we would call a narrative. And yes, technically there is a point there. When we’re talking about evolution, we’re not selling a story about the triumph of intelligent life slowly but surely culminating in us and continuing until we’re immortal transcendent beings of pure thought, as New Age inspired sci-fi would have us believe. Instead, we look at a nearly 4 billion year process of trial, error, random events, and odd twists and turns that managed to create the world we see today. True, to many people that’s not a satisfactory explanation for how we got where we are today and it deprives them of a sense of purpose and being divinely spawned for a noble cause.

But here’s the big question we should all ponder for a minute. Since when is it our job to make sure that facts fit in with the narratives people want to hear? Wouldn’t we just be lying to them if we misrepresent the data we collect and the research we conduct? And for what purpose? To make them believe us not because we have the data but because we cherry picked and massaged it for popular appeal? If the goal is to simply tell people what they want to hear, why even bother doing any science in the first place? Might as well just concoct a good story and run with that. This is why, as Bartlett notes, evolutionary biologist Jerry Coyne cites religious beliefs, not the quality of evolution as a popular narrative as the main culprit in evolution denial and he has the data on his side to prove his point. When he cites polls in which some 60% of Americans say they’ll just continue with their belief system no matter what they science says, that’s not even a red flag anymore, it’s a wailing alarm. If you really think that you’re going to get people who reject science to suddenly accept it when you just let them substitute their personal ideology for facts they don’t like, you are headed down the path to this…

At the very least, though, evolution’s weakness as a story creates a PR opportunity for creationists. For example, one Christian Web site tries to fit evolution into a standard fairy-tale narrative, telling the intentionally absurd tale of an amoeba’s transformation from salamander to monkey to man, all thanks to a character called Mutation who just waves a magic wand. It doesn’t read like it was written by someone with a background in biology, but it’s hard to disagree with the conclusion that evolution is a “strange story.”

Well of course it’s a strange story when it’s written by someone who has no idea what evolution is and tries to desperately wrangle it into a narrative of personal glorification, i.e. that humans are somehow the pinnacle of the evolutionary process or at least on their way towards it and our appearance was predetermined, or to turn it into a laughable parody of the facts. And of course it doesn’t fit into our tidy self-centered vision of nature, but then again neither do electrons, or black holes, or stars, or quantum mechanics which can technically violate causality according to a recent experiment. That’s the whole point of doing science, to find out what can and what does happen rather than weave a tale everyone involved finds palatable. Those so wrapped up in all the dogmas they hold so near and dear they will rabidly refuse to let them go no matter what, and treat something that challenges their views with contempt without even bothering to try and understand it, are just not going to care what the facts have to say and it’s their attitude that’s the problem here, not the data. As long as they don’t hear the story they want to hear, they’ll move goalposts, argue, and dismiss anything that we have to say out of hand no matter how much evidence we present. Further insulating them from facts by demanding that we give room for their favorite just so stories in science classrooms only makes things worse for everyone.

Just like giving a petulant child who throws an embarrassing temper tantrum in the middle of a store what he wants is a bad parenting strategy, placating anti-scientific crusaders by letting them do whatever they please, dismissing all the damage they do to public education and discourse as their inalienable right, is pretty much the absolute worst way to teach science. Next time the hypothetical spoiled brat wants something, he will just throw another tantrum in a public place to force you to submit. And next time anti-science crusaders want their preferential treatment from school boards and lawmakers, they’ll just engage in the same hysterics and paint any effort to teach actual science to potential future Babbages, Einsteins, and Darwins, as nothing less than a war on their very right to exist. Appeasement is not a valid strategy against those who believe that their word is to be treated as law and once in a while, they need to be politely but firmly told that while they have a right to go to whatever house of worship they want and pray to whatever deity their desire in any way they see fit, schools will teach objective, documented, verifiable facts to students, not serve as their indoctrination centers.

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When it comes to biology, everyone can name the key molecule for life as we know it. Scientists mine it for all sorts of tantalizing clues about our past and possible future while creationists effectively worship it as proof of a deity as some sort of programmer of all living things. But what if I and Ed Yong were to tell you that DNA isn’t the only molecule capable of passing down hereditary information and serving as a key mechanism for basic evolutionary changes? In fact, there’s a whole class of so-called XNA molecules in which deoxyribose can be easily replaced with a whole host of other sugars like cyclohexane, therose, hexose, and glycol to create new kinds of hereditary molecules called CaNA, TNA, HNA, and GNA, respectively. The X in XNA is basically just a placeholder for any sugar that will form a stable helix to contain the nucleic acids to be read. Considering that so many sugars can step up to bat and create a double helix enabling living things to develop and evolve, it’s actually kind of a mystery as to why deoxyribose won out at the dawn of time and prompts one to wonder if we would still be around with say, an ANA which used arabinose instead of the DNA we know and love today?

Now, oddly, the answer seems to be yes because they function the same way and there’s no reason why we couldn’t exist with such a substitution to our cellular chemistry. It’s too late now of course because a life form using an XNA wouldn’t be able to replicate with a DNA utilizing organism. In fact, the researcher who identified these possible permutations of hereditary molecules wants to use them to safeguard us from synthetic life, making sure that it could still be hearty enough to survive competition from bacteria that have been around for billions of years while being unable to actually interfere with our current ecosystem. And as Ed points out, the divergence doesn’t stop there as some scientists are adding even more bases to hereditary molecules to try and coax synthetic life forms into producing very unusual amino acids that would be of use to us. Now, this is all obviously pretty cool because this is quite literally tinkering with the foundations of life, both as we know it, and as we think we might know it, but what can it say about the future and the implications of this work? A very straightforward application could be in astrobiology and the probes sent to other worlds could be instructed to detect a wide array of sugars used in XNAs in soil samples, hopefully indicating some alien biota.

But there’s a potential for a different application. Today, we can engineer fairly harmless viruses which deliver small bits of interfering RNA to shut down gene expression in certain disorders, halting their progression to make them easier to treat. One of the ultimate possibilities of this siRNA technology is to keep cancer tumors in stasis, though considering the recent findings that each tumor may house more than ten different strains of harmful genetic anomalies, we need to figure out how to effectively customize them to attack all those different harmful genes first. It’s a tall order to be sure, but the important thing is that we have a plan and there’s a lot of research into this type of genetic engineering underway. Ultimately, this could even open to door to modifying our own gene signaling to drastically improve our quality of life with age, and perhaps even increase life span by manipulating the biology complicit in making us weaker and more prone to death. Nature doesn’t have the expiration date for an organism stamped into its genome which makes it much harder to delay death, but we know that after a while, the repair of wear and tear slows and damage continues to build up until we get weak enough to be taken out by something that might not have killed us if we were younger or a vital organ starts to fail after accumulating too much damage to continue working as it is. A thorough understanding of how genes and gene expression work can help us find ways to repair or even reverse all that damage…

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One of the big predictions made by evolutionary theory is that if given the selective pressure to do so, colonies of unicellular organisms will combine into multicellular organisms and start forming divisions of labor. Going from single cell, to cooperative colony, to a macroscopic organism with differentiated cells had to happen over several billions years to make the Cambrian Radiation possible. But how does this process work? For years, biologists tried to induce certain single celled organisms to merge into multicellular ones and came up with a number of interesting cooperative entities. However, actual multicellular behavior, i.e. the organisms acting as one being rather than a big colony, eluded them until now. After steering the selective pressures for a strain of yeast, a team of biologists from the University of Minnesota managed to evolve multicellular organisms which showed growth phases and simple cell differentiation, key traits of true multicellularity. While this experiment can’t show us how the very first multicellular organisms evolved, it does prove that it can happen, and that an environment that encourages something as simple as clumping can trigger a profound evolutionary shift.

Here’s what happened. Yeast growing in nutritious broth was allowed to get relatively comfortable and to start clumping into potential colonies. Then, every once in a while, the mixture was shaken and only the clumps of yeast that managed to stay together were kept. Finally, to induce multicellularity, the scientists focused on the clumps that best stayed together and took longer to reproduce as they grew. Within two months, there was an easily identifiable juvenile stage which the multicellular yeast had to complete before reproduction, and some of the cells adopted a faster lifecycle than others, decreasing in size and serving as reproductive cells. With a smaller size and shorter lifespan, they provided more spores even though it necessitated a shorter life. They were essentially adapting to die faster for the benefit of the larger organism of which they were now a part, an extremely important trait of differentiation in multicellular life. Of course there’s a huge difference between this and completely different cellular shapes and structures tasked with very specific jobs, but as the authors note in their paper, this is just after 60 days. The level of differentiation we see in macro life had to take millions of years to even become possible. Seeing specialized precursors of gametes evolving in months is a really big deal already, especially when coupled with the fact that the resulting yeast had a juvenile phase.

With this starting point, one could imagine subjecting the new multicellular organism to nutrients best suited to feed an internal colony of mutated cells which could be induced to share the products of their digestion and thus forming a digestive tract, or coating the experimental organism in cells that will keep it insulated from an external antagonist, creating a shell, and so on. We’ve often thought that cooperating unicellular organism will be able to coalesce and work together and this experiment shows that we were right. Yes, perhaps the yeast has some mechanisms encouraging multicellularity and that’s perfectly fine because it shows that the ability to combine with other cells into a new organism can evolve in unicellular entities on its own, then lie dormant until a selective pressure makes it a net benefit. In summation, this is a very neat experiment which can start new lines of inquiry into differentiation and development, something that will better illuminate why our bodies and that of all other macroscopic animals can work and develop the way they do. Sure, this may not be a one for one repeat of how multicellular life really evolved, but that’s not the real goal here. What the scientists want to see what mechanisms are at work in creating multicellular life and whether their ideas for how we could’ve went from one cell to trillions over the span of 3.5 billion years have any merit. Increasingly, it seems like they do and while we may never know the exact sequence of events, we’ll have some really, really good ideas.

See: Ratcliff, W., et al. (2012). Experimental evolution of multicellularity PNAS DOI: 10.1073/pnas.1115323109

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Biologists seems to have a love-hate relationship with evolutionary psychology. Some think it’s terrific that we apply evolutionary reasoning to different questions about life and living things in general, others see it as the brainchild of sloppy thinking or just thinking way too hard. Personally, though I’m not a biologist, reading a lot of evolutionary psych investigations pushes me towards the opinion of the latter group. It seems that virtually every supposedly scientific finding about dating, sex, and social habits that produces a buzz in the media and prompts lists of "scientific reasons why blank" you see on so many pop sci and entertainment sites, will also generally support stereotypical gender roles or vast blanket generalizations such as: men were hunters while women had children and ran the caves/tents/houses so all their behaviors derive from that arrangement.

A while ago, Greg Laden struck out at evolutionary psychology’s propensity for gender role assignments, and now, after reading a sloppy paper on women’s supposed adaptations to avoid rape during ovulation, PZ went into a rant about the major shortfalls of the field. And you know what? He’s absolutely right. You can’t have a fruitful field of research by focusing on one particular feature of an organism’s body or behavior, then focusing all your efforts on explaining why and how it evolved even if there’s really no apparent reason to pay so much attention to that feature. Well, I suppose you can, but all you’ll end up with is pseudoscience draped with some scientific language borrowed from evolutionary biology and backed up with tests which don’t say a whole lot of anything about the topic or fail to consider the long and complex evolution of human societies in the process of simplifying something very complex or elevating something inconsequential.

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Former science writer John Horgan isn’t happy with the media coverage of Venter’s newest experiment with synthetic genomes and dead cells, and while downplaying what he sees as needless, unwarranted media hype, managed to take out his displeasure not only on pundits and philosophers trying to make a story where one doesn’t exist, but the scientist himself with a rather unflattering description of the biologist and his efforts in his guest post at SciAm. In fact, that dig at Venter’s ability to get press coverage is his opening hook…

Venter is the Lady Gaga of science. Like her, he is a drama queen, an over-the-top performance artist with a genius for self-promotion. Hype is what Craig Venter does, and he does it extremely well, whether touting the decoding of his own genome several years ago or his construction of a hybrid bacterium this year. In a typical Venter touch sections of the bacterium’s DNA translate into portentous quotes, such as this one from James Joyce: “To live, to err, to fall, to triumph, and to re- create life out of life.”

Now, is it just me or does Horgan have some sort of a bone to pick there? Sure, Venter is well connected and well funded, his projects are extremely ambitious, and he likes to set bold goals. However, he doesn’t pitch a pet project as a potential solution to all universal problems like Wolfram, or just talk a big game, aiming for the sky while still learning how to walk, like de Gray. He lays out his goals quite clearly, focuses on the actual science at hand, and produces tangible results. His presentation at TED in 2008 touched on the potential of creating synthetic life to solve global problems, but he didn’t imply that the technology was almost there and if we want to see it come to fruition, we should just watch him and his team. Ok, so he put in a watermark with a high brow quote into a synthetic genome, so what? What would Horgan rather have him do? Add “this is a test genome” and nothing fancier than that, otherwise Venter is an unabashed glory hound?

It seems that Horgan is taking out his frustration at the sensationalistic media coverage of scientific topics, an unfortunate norm nowadays, at a scientist who gave them a great story from which to spin tales of the future and fantastic proclamations. While he emphasizes that Venter didn’t actually create new life in the lab, neither did Venter and the only people who did were reporters and philosophers, who tend to either lack the scientific skills to adequately interpret what actually happened, or want to make a big pronouncement despite lacking a reason to do so. And to counter them, Horgan decided to bend the story to the other extreme and plays up the mysteries of life’s origins and how far we seem to be from understanding how living things appeared.

[Bioethicist] Arthur Caplan declares that Venter and other scientists have dispelled the notion that life “is sacred, special, ineffable and beyond human understanding.” Wrong. We still have no idea how life began, or whether life exists only here on our lonely planet or pervades the cosmos. One of the great ironies of modern science is that as we gain more power over life, it remains just as fundamentally mysterious as ever.

Sorry Mr. Horgan but no. Scientists and many of those who follow their work understand life as a very complex biochemical reaction, a view which already demotes life from its post as a sacred, incomprehensible enigma so we can study it in the lab. Whatever you say about Venter’s experiments, they do help us get a much better idea of how life began by experimentally reducing living things down to their most basic parts, drawing a more defined line between living and non-living. When we know what chemistry has to take place in order to make a living, self-reproducing cell, we can further break it down in its core components and figure out some possible scenarios of how the building blocks of our universal common ancestral population came together, as well as from where these building blocks might have come.

We will probably never know exactly how life got started on Earth, but we’re seeing some glimpses as to how that may have happened thanks to experiments done by Venter and his team, as well as those what build on his work. There are many years of work still ahead, but to pretend that we’re just as ignorant about the origins of living things as we were some 50 years ago, when DNA was just being formally identified for what it really was and the concept of synthesizing genes was still the stuff of wild, science fiction comic books, is simply no longer an option. At least not an intellectually honest one anyway.

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When talking about the origins of life, the term universal common ancestor gets thrown around quite a bit. But did all life really come from a single ancestor? Considering that genes can swap species, could there be the intriguing possibility that instead of a single common ancestor there was an entire pool of simple organisms swapping genes until the precursors of the very first biosphere finally appeared after tens of millions of years of mutations and selection? This idea of multiple common ancestors sharing the primordial soup got editors at New Scientist to make their now infamous cover picturing the modern version of a Tree of Life in Darwin’s notebooks with a provocative title asking whether the naturalist who came up with the idea of natural selection was wrong and the tree of life is actually more like a dynamic web with plenty of horizontal gene transfers. And while this may sound plausible, what does the science say about the odds of this actually happening?

Well, as a statistical analysis of 23 proteins in 12 species indicates, the idea of multiple UCAs is actually very unlikely and a single common ancestor to all life which evolved in an environment where hybrids could swap genes across the species barrier every once in a while, fits the observations 103,489 times better. And even if his model didn’t allow gene swapping, biochemist Douglas Theobald still found that a UCA is 102,860 times more likely than multiple ancestral pools. So in other words, all life on Earth is over 100,000 times more likely to trace its lineage back to a population of microorganisms that appeared roughly 3.5 billion years ago rather than to a web of many unknown common ancestors. In fact, when taking species from the biological domains of bacteria, archaea and eukaryotes and compare how well their proteins would match if each evolved from a unique ancestor, Theobald found that the odds of them independently matching each other to the degree they do today is approximately 1 in 1 followed by 2,680 zeroes. Or in other words, virtually impossible,

Why are we dealing with a 1 in 102,680 probability of multiple ancestral populations? If we look at the genetic sequences of multiple species with similar genomes, it takes less mutations to account for the differences in the proteins they generate if they had common ancestry than it would be if they had independent origins. With more required mutations, the odds against a particular scenario quickly rise. But hold on, are only 23 proteins enough to make conclusions like this? Wouldn’t more proteins make for a more valid analysis? Not really. If a limited number of proteins across just a dozen species in three domains is already yielding data like this, an addition to the sample pool is either not going to alter the odds by a statistically significant amount, or give us an even higher degree of commonality since models which hypothesize an independent origins would have a lot more mutations to match. Unless we found a shadow biosphere which seems totally unrelated to anything we know today, odds are that the Tree of Life is going to remain the dominant framework for explaining why all living things on our world are closely related, even after billions of years of selection.

Oh and there’s another interesting side note to consider. Theobald contributed quite a bit to Talk Origins and the Panda’s Thumb, debunking his share of creationist pseudoscience. So just for the hell of it, he thought he would test how likely it is that humans aren’t actually related to anything on Earth and appeared out of the blue as far as nature is concerned. So yeah, about that… Remember how I just called 1 to the 2,680th power pretty much impossible? Well, the odds of humans spontaneously appearing on our planet are even worse. In fact, they’re a ridiculously unbelievable 1 in 1 to the 6,000th power which is so much more unlikely than a multiple ancestor model, there isn’t even a name for a number this big. Looks like the buffoons playing scientist at the proudly ignorant Uncommon Descent have some more denying to do, and this time, in the face of absolutely staggering odds against them, odds, which unlike Hoyle’s biologically invalid assumptions, are based on a real data set from real genomes of real living things, rather then Dembski’s imagination.

See: Theobald, D. (2010). A formal test of the theory of universal common ancestry Nature, 465 (7295), 219- 222 DOI: 10.1038/nature09014

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What do brains and computer chips have in common? Not that much. Sure both use electricity, but in neurons the origin of electrical pulses is chemical while for computer chips it comes from electrical currents. Neurons are highly plastic, rearranging their connections to adapt to new information while computer chips are locked in their arrangement for their entire existence. But one thing they do share is the pattern of connections in their overall structure, specifically both brains and computer chips use the shortest and most efficient pathway they can to avoid the costs associated with taking long detours for the signals to get to their destination. Evolution and chip designers seemed to have reached the same conclusions when bumping up against the same very basic and very important limits, says a recent research paper from a small international team in PLoS.

After examining the brain structures of humans, extremely well understood laboratory nematodes, and some run of the mill computer chips, they noticed that two very interesting things about both as noted in a write-up of the study by Science Daily

First, the human brain, the nematode’s nervous system, and the computer chip all had a Russian doll- like architecture, with the same patterns repeating over and over again at different scales. Second, all three showed what is known as Rent’s scaling, a rule used to describe relationships between the number of elements in a given area and the number of links between them.

The first finding confirms the research being done on intelligence and cognition in insects and mammals. A brain doesn’t necessarily evolve new structures as it increases in size. Instead, we see a repetition of basic patterns and more intricate interactions between them. The current idea is that larger animals evolve a larger brain to control their bigger bodies and whatever cognition they get out of that is a positive side-effect. When it comes to humans, our brain has grown in part because of a crucial set of mutations and natural selection’s emphasis on outwitting predators in the environment where we evolved. In other words, our brain is more of a scaled up, over-clocked version of what many mammals already have. Again, this fits quite well with what we would expect to see for a nervous system which evolved over millions of years of selective pressures favoring higher intelligence and abstractions like strategy, memory and creativity.

The second finding also seems to confirm something we know about evolution, mainly that natural selection tends to trim down waste and excess if it can and over a long period of trial and error, it will eventually arrive at efficient solutions to basic problems. We can see this in how DNA is packaged in our cells and now, how our nervous systems end up supporting the shortest plausible signal pathways to run our brains more efficiently. If it didn’t, our nervous systems would be too expensive to run and fewer of us would’ve survived our feral days in the plains and deserts of Africa and the Middle East. Of course this shouldn’t be taken to mean that we run at peak efficiency, especially since many signals in the brain misfire on a routine basis and not every pathway is necessarily optimized to the level of a microchip. The authors also stressed that they were working with too few nervous scans to pin down just how close the relationships between brains and chips really are, so while their initial findings are both promising and seem to make sense, this is an area of research which needs to be continued and expanded in the near future, hopefully with much greater sample sizes.

See: Bassett, D., et al. (2010). Efficient Physical Embedding of Topologically Complex Information Processing Networks in Brains and Computer Circuits PLoS Comp. Biology, 6 (4) DOI: 10.1371/journal.pcbi.1000748

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Usually, when this blog mentions creationists, the emphasis tends to be on fervent Christian fundamentalists like the staff at Answers in Genesis, or on promoters of theistic pseudosciences like the Discovery Institute and the Templeton Foundation. But we shouldn’t forget that Muslim creationists can be just as bad and are in fact noteworthy players in global evolution denialism. In an effort to demonstrate the problems with creationist arguments across the spectrum of faiths, today we’ll be taking a look at a truly odd paper written by Professor Pallacken Abdul Wahid, who has a PhD in agriculture and a passion for armchair theology. According to a few of his musings, the universe is actually a computer program ran by Allah and he intends to demonstrate this concept with such a thorough mangling of genomics, he will literally lead us back to the Garden of Eden in a supposedly scientific paper about the structure and function of chromosomes, and hereditary information.

Ok, we’re getting a little ahead of ourselves here. To properly appreciate Wahid’s attempt at shooting down the modern understanding of biology, we need to start with his arguments. First he says that an organism’s cells all carry the same information but come in different types, something he insists that genetics can’t explain. It’s pretty clear that somebody hasn’t looked up how differentiation happens during an organism’s development. There’s a number of very accessible popular science books and shows which talk about genetic toolkits and how turning certain genes on and off produces an impressive variety of cell types which go on to form organs and body parts. So far, so bad. Then, we’re hit with another terrible argument. Wahid notes that after death, an organism’s genetic code is the same as it was in life, therefore, genetics can’t account for things like life and death. And this already ridiculous argument is made even worse with the following display of ignorance…

Added to that is the failure of the synthetic genome to spring to life. A team of molecular biologists at the J. Craig Venter Institute, U.S., artificially produced the complete genome of an organism [ ... ] This is a landmark achievement in biology .. it proved [that a] genome cannot come to life implying that genome is not genetic information. This experimental evidence also confirms that life cannot be produced from non-life.

Talk about not even wrong. Since when has death been genetic? Organisms die when their bodies wear out, not according to a killer gene that determines lifespans. Now, if Wahid tackled the lack of a fixed lifespan limit in our DNA, I could see where he would be able to take this line of reasoning. But just pointing out you’ll find a living organism and its dead counterpart carrying the same genes and considering it a good enough base for stating that genetics can’t explain life or death and therefore, the science behind it is terribly flawed, could only show a total lack of relevant knowledge on the author’s part. That goes double for his argument that if you put together a synthetic genome, this genome will come to life, and if it doesn’t, you’ve disproved abiogenesis. It’s an absurd notion from start to finish because hereditary information is very important in organisms, but so are all the other biological structures they have. DNA by itself is a very long molecule carrying hereditary patterns. It has to be interpreted and its codes translated into proteins. Without machinery for that, a replicated genome is not going to suddenly come to life as Wahid seems to believe it should.

So what does the good doctor make of our chromosomes and the DNA contained within it? That we’re all “bio robots” and the nuclei of our cells get divine programming to carry out daily functions. Just to put this in proper perspective, we have a person who doesn’t know the difference between an organic molecule and a living cell go forth and rule out abiogenesis on the basis of of an experiment in which DNA didn’t get up and do a dance in a test tube, but it’s not too big of a stretch for him to consider that Allah is downloading divine software to the chromosomes in our cells. Talk about having your head in the clouds. And then, just to add to the combination of ignorance and sweeping, wild claims, he decides to throw in the idea that human chromosomes look like a pair of ribs and therefore, when Genesis and the Qu’ran talk about Eve coming from Adam’s rib, it’s really just a metaphor for Allah booting up the first woman’s “biosoftware.” I’m just going to say that if you were to look at an actual micrograph of a chromosome, you would not be thinking of little, floating ribs and leave you to come up with all the ways to count the approximate amount of absurdity in his statements.

Obviously, the world of Dr. Wahid and that of actual biologists are very, very different. It’s a fanciful place where gods download mysterious “biosoftware” into rib-shaped chromosomes and strands of DNA are required to routinely come to life on their own to prove the validity of genomics. It’s also wrong from top to bottom and just begs me to issue kids a warning to stay in school and keep studying for those science tests. Though maybe, pass on Kerala Agricultural University, since they seem to have a given a PhD to someone who clearly doesn’t know how to use it or even how to do some very simple research for a public paper.

[ original story via PZ Myers ]

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