Oh No! We're Eating the Offspring of Clones!

In a class I'm teaching right now, we've been talking about the nature of science and also about the common misconceptions, misunderstandings, and simple ignorance that pervades our mainstream media. Yesterday, I ran across this article on yahoo news: Clones' offspring may be in food supply: FDA.

The first line:

Food and milk from the offspring of cloned animals may have entered the U.S. food supply, the U.S. government said on Tuesday, but it would be impossible to know because there is no difference between cloned and conventional products. (emphasis mine)

I think this is a perfect example of how issues of real scientific import become muddled sometimes by skimpy reporting and usually by a failure of most American readers to actually understand the complexities of scientific issues (even when these issues may have direct impacts on their own lives and health).

The article itself isn't that bad - it does mention that:

The U.S. Food and Drug Administration said in January meat and milk from cloned cattle, swine and goats and their offspring were as safe as products from traditional animals.

Don't get me wrong, there are many, many issues still left to be studied and understood regarding genetically-modified organisms, as well as issues related to animal rights, biodiversity, and economics with regards to cloned animals.

But when your reporting says things like

"It worries me that this technology is out of control in so many ways," said Charles Margulis, a spokesman with the Center for Environmental Health. The possibility of offspring being in the food supply "is just another element of that," he said.

it tends to strike me as a bit fear-mongering and I can instantly see a thousand people reading this one line and abruptly turning their minds off to the possibilities. "Oh no. It's out of control. We've gotta stop it all now. Stop the research. What am I eating? Stop playing God. Stop!"

I am not trying to argue the position that "we should eat cloned cattle" - mainly because the benefits aren't that clear to me (it seems mostly economic at this point). But I DO know that, as the article states, the offspring of a cloned animal is identical to it's "parent", as far as its chemical makeup and safety. I find too often in the media that the technologies of genetically modifying organisms and the relatively simpler technology of cloning are confused with one another. Adding genes or changing genes in an organism is a far different beast from simply creating a new animal using the genetic material of another. The FDA cannot tell cloned animals apart because there is no difference. From a health standpoint, there is no reason whatsoever to eschew ingredients from the offspring of cloned animals.

I think that there are many potential and amazing opportunities to be found in modifying organisms - for food nutrition, for medicine, for things like sustainable energy production (though I am less than enthusiastic about the modifications being done for herbicide and pathogen resistance). However, much research needs to be done still, especially with things like lateral gene transfer from crops to the environment. The important point is that I think the public needs to become much better informed about the specifics of these technologies.

The article states

"We must also carefully consider additional factors such as consumer benefits and acceptance ... and research in the U.S. indicates that consumers are currently not receptive to ingredients from cloned animals," she said.

Why aren't consumers receptive to cloned animal ingredients? It's certainly not because of a sober look at potential impacts to biodiversity and animal rights, as examples.

No it's because they don't really know what it means. It's gut instinct. "Frankenfood." FEAR

(FYI: The title is intentionally ironic)

Update: Some posted the original article on Digg. The poster said "I don't want to eat meat anymore". The first commenter said:

"If this meat is no different than conventional meat, why don't we just throw is dogs and cats into the food supply and solve the stray problem. They are after all meat also and are considered delicacies in many parts of the world."

Somehow he got from "there is no difference between offspring of a clone and the original" to "scientists claim all meat is identical", or something like that.

Sad.

Tangled Bank #113: A Labor Day Carol

The next edition of the Tangled Bank blog carnival, #113, is now up over at En Tequila Es Verdad.

The intro is one of the more entertaining carnival intros I've read as of late.

My favorite part (aside from the many awesome links within it), is the description of the time-traveling narrator's pant besuited appearance before Charles Darwin:

Roughly an hour's worth of explaining how a woman in pants waving a monstrous electronic paddle had come to appear in his study ensued before I obtained an answer to my original question.

Go check it out. My own post on a cool little piece of evolution research is included.

Another Step in the Evolution of Humans and Apes from Ancestral Mammals

One of the most fascinating lines of research within the field of evolutionary biology is the search to find the genes that changed at the split between ancestral mammals and our own closer ancestors, the great apes.

In a fascinating new study in the August 8th edition of PLoS Genetics, Lia Rosso and colleagues have detailed specific changes in a single duplicated gene in apes and humans. Their data reveals what may be a common path for evolution: duplication of a gene with a specific function, a change in the duplicate that allows it to change its location within the cell, and further changes in the specific function of that gene.

There are several interesting things that I took from this study. First, the genes they study are GLUD1 and GLUD2, enzymes involved in glutamate metabolism, which in itself is less interesting to me (just a personal disinterest in metabolism - no offense to you metabolism folks). What's simply astounding to me is the method through which the second gene came about - a method of duplication I sometimes forget.

GLUD1 is present in all mammals, while previous research has shown that GLUD2 arose through an amazing process of duplication that departs from the simple genomic duplication methods we often think of.

Here's a quick primer for you non-biologists that will help you understand. Most vertebrate genes are actually broken up along a strand of DNA. That is, there are sequences (called introns) within the gene that are not involved in coding for the gene's protein.

Imagine that this sentence is a gene: BIOkzkfkjLOGYskrzsISkzskjzsCOgkttkzjOL.
In this case, imagine that the product of the gene is "BIOLOGY IS COOL".
The gobbledegook between and within the words are the introns that are cut out before the product is made. The question of why the nonsense sequences are even there is a whole other story that we won't consider here.

OK...so now we have our gene - let's call is BioCool1.

One other point you must know - DNA genes are read and "transcribed" to RNA, which serves as a "message". The RNA message is then read to make the protein. Okay?

When the BioCool1 gene is transcribed to RNA (which is then used to make the protein), those nonsense gobbledegook introns are removed so that there are now RNAs floating around the cell that read "BIOLOGY IS COOL", without the nonsense introns.

Now, you may have heard of some viruses called "retroviruses", such as HIV. That means that they have enzymes that can take their viral RNA genome, "reverse transcribe" their genome into DNA, and then insert the DNA version of their genome into our own genome. Thus these viruses make themselves a part of the host organism, and the host genome now produces tons of viral RNA and proteins.There are more levels of complexity in this, but to keep it simple we'll just consider retroviruses.

Imagine if those viral enzymes take that BioCool1 RNA with the introns cut out, turn it into DNA, and then insert it back into our own DNA genome. What we have now are TWO versions of the BioCool gene DNA in our genome: the original BioCool1 (which has all the nonsense sequence within it, and a new version, BioCool2 (which only has the "BIOLOGY IS COOL" sequence).

Well, this is how GLUD2 was originally made in ape and human ancestors from the GLUD1 gene. Pretty amazing, no?

What the above researchers further showed is that while GLUD1 protein can be found in multiple places in a single cell (in the mitochondria and cytoplasm), GLUD2 underwent a single amino acid change that made the protein stick only to the mitochondria. Using sophisticated analyses, they showed that this change occurred soon after the gene was duplicated 18-25 million years ago, and that the change was then positively selected for (meaning that animals with the change were somehow "more fit" than other individuals). The gene concurrently underwent further changes that altered the specific function of the protein, and it is suggested that the changes were involved in brain function (specifically in metabolism of the neurotransmitter glutamate).

So...in summary, this study reminds us of a pretty cool mechanism for duplicating a gene and positively selecting it for function in specific subcellular locations, and it gave us one more glimpse into the changes that have resulted in the evolution of the amazing complexity of the human brain.

---

image from psychology.wikia.com

Carnival of the Godless #98

C. L. Hanson over at Letters From a Broad: The Adventures of a Friendly Ex-Mormon Atheist Mom Living in France Switzerland (I love that title) has composed the 98th biweekly edition of Carnival of the Godless, a blog carnival containing a myriad links to thoughts on atheism or tangentially related topics. This edition is particularly well done, and contains hours worth of edifying reading and links to make your brain cells hurt.

Graciously included in this latest edition is my own previous post, Hope in the Black Void of the Unknowable, in which I muse on whether we really want every human on earth to see the Universe and ourselves as science sees us, namely "no more than blips of energy in an inconsequential cosmic blink."

Check it out, and if you have your own musings on issues relating to an absence of God, go to Carnival of the Godless and find out which blog is hosting the latest edition and submit your stuff to them.

Hilarious Conversation with E.T.

Today on Digg, an article was linked in which it talked about some astronomers who think that we will likely contact extraterrestrial civilizations within the next two decades.

However, the point of this post is to highlight what may well be the funniest comment I've ever read on a Digg post. The second comment down, by someone named Dumbledorito wrote:

"Hey."
"Hey."
"Got warp drive, or something?"
"Nope. You?"
"Nope."
"That's too bad. Our world is kinda fucked."
"Ours, too."
"Want to trade porn?"
"Why not?"

Priceless...

Will Tequila Plants Fuel Our Vehicles?

I read a couple of interesting articles today about a plant of which I have become very fond: the Agave plant. The first is Drink it or Drive it: The Promise of Agave for Ethanol, by Sarah Lozanova, and the second is Mexico & Agaves: Moving from Tequila to Ethanol

For you non-botanists, the Agave is a cactus-like plant that grows in semi-arid lands such as Mexico and the American southwest. Some species are known as “Century Plants” because of the exaggerated claim that it takes them a century to bloom (which is actually more like 25 years). Of course, any avid tequila drinker also knows that this is the plant from which the infamous killer of inhibitions is distilled.

As Sarah Lozanova of CleanTechnica.com writes, the Agave may be one of many potential saviors in the world of ethanol-based fuel production. In her article, she talks about the fact that Agaves contain very high sugar content, which make them an excellent source for producing ethanol. They also have very high cellulosic biomass, which may up their potential use by many factors, assuming we can perfect a method for making ethanol from cellulose.

However, ignoring the cellulosic content, Agave has many other characteristics that may make it a prime crop for ethanol production. For one, it requires very little water or irrigation. It also can grow in almost any type of soil because it is a “nitrogen-fixer,” meaning it essentially fertilizes its own soil from the air, leaving the soil in better condition than it was before.

Thus, considering the vast expanses of semi-arid land in the southwest and Mexico, it might be cultivated without having major impacts on traditional crop farmlands. In many ways, it is even better than using sugar cane, which as is well-known, promotes deforestation of rain forests.

There may or may not be other issues with using Agave, but it seems to me that it very well may at minimum become a small piece of our energy-independence puzzle. In my own opinion, though I am about as far from an expert on economics and trade politics there is, my guess is that this could have at least some impact on the whole immigration issue. I have no idea how many jobs would be created by a fuel-fueled increase in Agave cultivation, but I can’t imagine that it would be insignificant.

As a side note, the images you see above are of my own Agave plant. Almost forty years ago, my grandmother’s sister stole a plant from across the border in Mexico. My grandmother has been growing the original plant in Texas ever since. In 2000, she gave me an asexual offshoot from that plant (they send out many baby side-shoots that will grow into full plants). I now have half a dozen Agaves from the one she gave me. Without a doubt, it is the plant with the most sentimental value for me.

Science Takes Another Step Toward Understanding Human Evolution

In a previous post I highlighted one of the great questions facing science today: how did we evolve and what specific genes make us different from our cousins in the animal kingdom?

In a new study reported in this month’s issue of PLoS Genetics, Carolin Kosiol and colleagues have demonstrated the most complete analysis of the human, chimpanzee, macaque, mouse, rat, and dog genomes to date, highlighting many genes and pathways that have contributed to our own evolution as mammals and primates.

Evolution fundamentally occurs at the gene level. If a gene becomes mutated, thus making an organism (or population) more likely to pass on that gene, that gene can be said to have undergone “positive selection.” The environment has positively selected that gene to become more prevalent.

Just to give you a very quick primer on gene evolution, one thing necessary to understand is that all mammals (and indeed all vertebrates) contain a large number of genes that we share in common. For instance Tbx20, a gene involved in heart development (which I used to study), exists in all organisms from flies to humans. The function of this gene is the same or similar in these organisms, though there are many specific differences between them as well.

It is these genes that we share with the other organisms that these researchers compared. What the authors of this study have done is to look at the differences in the sequences of these mammalian genes to determine which sets of genes have changed the most – i.e. which genes have undergone positive selection during evolution. They highlighted several pathways that have undergone the “strongest” positive selection, such as defense/immunity, chemosensory perception, reproduction and taste perception.

Surprisingly, to me, they did not find pathways and processes in the brain that have a high number of positively selected genes. It seems to me that this can be explained by a few different possibilities: 1) only a few specific genes have evolved strongly, but these few genes resulted in huge changes in the brain, 2) new genes have arisen (which were not looked at in this study – again, only genes that we share were compared), or 3) the brain genes that changed weren’t exclusively part of “brain processes” (for example, the gene I mentioned above, Tbx20, is involved in both heart and brain development).

Regardless, this is a very interesting study, and it brings us one small step closer to understanding what exactly makes us who we are as humans, as primates, and as mammals. And it opens us to new questions of how these specific genetic changes evolved in the first place.

Camp Inquiry on NPR

There is hope for skepticism, reason, and science in America yet! Today on NPR I heard an awesome story about a camp called “Camp Inquiry” (read the story here). It’s a summer camp for kids ages 7 to 16, in which instead of learning about the bible as in bible camps, they learn how to use skepticism, empiricism, and logical reasoning to guide their own knowledge of the world and their development.

And it’s about time. These kids get to have fun and do all the cool things I can remember in cub scout camp, art camp (Arts Encounter), and biology camp (called Wet-n-Wild – what a dork was I?). They also have deep philosophical discussions, look at the stars and planets, study fossils, and most importantly, bond with other children who have inherited or developed a skeptical mind.

I think this is a fabulous idea. I only wish that there were such summer camps for adults.

On that note, why the hell can’t we have a culture in which adults go to summer camp as a normal part of adult life? Summer vacations hardly compare with the experiences of camp - meeting new people at a place far away from home, learning new things, gaining new experiences.

Maybe we should institute a new cultural tradition. Every summer, we get one week off to go to adult summer camp. Hey, there could be a whole multi-billion dollar industry surrounding it.

I know, I know – what about money, jobs, kids, time, blah.  Of course it would never be practical, but hey – can’t a kid masquerading as an adult dream?

Amazing Cells in a Dish

I grew these mouse embryonic stem cells on a plate, and through various molecular trickery, I made them turn in to the crazy cell types you see here. (Click for larger images)

Check out the next two images. They are the same cells viewed in two different ways (normal light, and epifluorescence).

Long neuronal axons stretch across the dish below.

Two beautiful connected cells.

Science Discovers a New Sense

It now appears that the lowly worm, Caenorhabditis elegans, has evolved a new sensory perception heretofore unknown to science. In the current issue of PLoS Biology, Stacey L. Edwards, Kenneth G. Miller, and others have shown that these nematodes can detect ultraviolet light using receptors completely unlike any other light receptive molecule in visual systems. In fact, this receptor (cleverly called LITE-1) is more similar to taste receptors in worms and in flies than pigment molecules in other visual systems. It remains unclear how the ultraviolet signal is transduced through the worms receptor to activate the worms’ nerves, however they have eliminated the possibility that it is only heat that they the worms sense. Regardless, it seems that evolution has again demonstrated the cooption of an existing system (in this case – taste), to create an entirely new system (UV sensing).

This serves as yet another example of a peephole into reality that should make us envious of our animal brethren. So let us add “tasting” light to the list, which now contains pit viper infrared, electroception of fishes, magnetoception of birds, and echolocation of bats and cetaceans.

Check out an excellent summary of the article here, or access the primary research article here.

23 Things Science Can Tell Us about Life, the Universe, and Everything

Ever since the evolution of the sensory neuron, organisms have been using the these amazing peepholes into existence to direct the course of their lives. Now, humankind has elevated the role of these senses, and even created technological extensions of them, in order to find order and true knowledge of this Universe in which we exist. We are all scientists looking at the world through our own tiny peepholes, attempting to find our place within it. We have sought to understand what we are made of, what drives our constant fight against entropy, and what defines us as thinking, living entities. Who knows what the future may hold or what constraints will be placed on our knowledge, whether through considered intellect and experience or through societal and cultural pressures? For the purpose of this article, I am ignoring any social, cultural, or religious implications or constraints that may face the endeavors of science. I simply ask: what questions remain about our selves and our reality that science may theoretically be able to answer in the future?

Some of these can naturally be considered sub-questions of others, while some may have sub-questions already included within them. As in most scientific knowledge, it is all interconnected. If you think of something that you feel should be added to this list, please leave a comment. I will gladly add it to this list if it is something even remotely answerable in theory. It can be in any field of science you wish.

1. What exactly makes us different from our animal cousins?
   
   With the completion of the human genome project, we now know that at the DNA level, we are 96-98% identical to our closest cousin, the chimpanzee. Scientists around the world are now scrambling to decipher what exactly in that DNA defines us as human and what separates us from the rest of our animal brethren. We have far yet to travel. It appears now that only about 1.5% of our genome encodes for proteins; the rest of it is often (and inappropriately) called “junk” DNA. We have deciphered the function of only a fraction of the protein-coding genes. Furthermore, many of the differences between chimps and humans lie within this non-coding DNA. The coming years and decades will yield much knowledge as to exactly which genes have evolved in the hominin line, which regulatory regions within the non-coding sequences have changed, and which structures in the brain and other organs define our differences. We already have a sizeable list of genes that putatively separate us from apes. However, there is still much work to be done.
   
   
2. What is the nature of the mind? How do the emergent properties of consciousness arise from the underlying interactions of synapses and neural pathways in our brain?
   
   This one is going to take a while. Eventually, however, we must assemble a complete working knowledge of all genes and all of their functions and interactions. We will combine our knowledge of molecular biology with our knowledge of cell biology. Over this synthesis, we will layer our understanding of neuroscience and cognitive psychology. We must take into account the existence of memory, emotion, learning, sense perception, and every other integral process or function of the brain. The question is: will the underlying structures and functions of all microscopic and macroscopic aspects of the human brain allow us to predict and explain the emergence of consciousness? Only time and science may tell.
   
   
3. What is love, hate, and emotion?
   
   Scientists have largely answered this question already, but as with most neuroscience, the details remain fuzzy. It is quite clear from decades of research that everything we feel, whether it be sensation or emotion, is mediated by the release of molecules, largely neuropeptides, between synapses in the brain. Dopamine, serotonin, epinephrine, and a large cadre of other small molecules act as the signals between our brain cells. Our understanding is growing by piecemeal, but as with the emergence of consciousness, soon we will hopefully be able to synthesize a complete model of emotion, including not only happiness, anger, sadness, joy, fear, and courage, but also spiritual experiences, amazement, and euphoria.
   
   
4. Who am I? What is the self?
   
   This may be seen as more of a philosophical question than a question that science can answer, and there are obviously huge aspects of this question that are inherently untouchable by science. However, I think that if we can understand all aspects of neuroscience and cognition, and if it turns out that we can predict and explain the emergence of consciousness from the underlying levels of complexity, then a full understanding of what defines the “self” may be a natural outcome. We will have a full synthesis of all aspects at all levels of the human brain, and it seems likely that we will then be able to define the “self” as a construct containing everything within the model. That is, you are the sum of all your parts, biochemistry, memories, senses, experiences, feelings, and the emergent properties themselves.
   
   
5. Can artificial intelligence have consciousness?
   
   No doubt, this question may be answered sooner than we think. The field of artificial intelligence is ever expanding, and as the complexity of our computing systems and programming grow, so too may that complexity lead to emergent properties that we may define as consciousness. A better question is perhaps: how long will it be before a computer or robot passes the Turing test (a conversation in which the human cannot tell whether he or she is talking to a human or a machine)?
   
   
6. Can a single human consciousness be replicated or simulated by computer or another organic form?
   
   This is almost the same question as number five, though it has a slightly different focus. This question could be reworded: if we can understand all aspects of consciousness and “self,” and if we have the computing power or organic synthesis power, could we theoretically “download” a human consciousness into another brain or into a computer. It’s the classic sci-fi dream. Who knows whether this is even theoretically possible? It would certainly take an almost unfathomable level of complexity of circuitry. In all likelihood, any specific consciousness or self would be too defined by the molecular and perhaps even quantum properties of its own constituent parts. I cannot really conceive of humanity becoming so adept at manipulating the physical world that we can completely mimic every neuronal connection and interaction in the brain. But then again, this very thought may be considered small minded several generations from now. There are also the philosophical issues of whether the “self” would truly be transferred. Nonetheless, I think this is a mind boggling question that may just be answered by science. Who wouldn’t want to be made virtually immortal?
   
   
7. What is the nature of memory? How is it stored in the brain?
   
   Here’s what we know: certain structures such as the hippocampus and amygdala are integrally involved in memory. In addition, much research is going on at this very moment in an attempt to define the method in which memories are encoded. Current results have shown that memories are likely encoded by the formation and connections of specific synapses (neural connections). There are an estimated 60 trillion (that’s 60 million million) synaptic connections in the brain. Hopefully, we will soon understand exactly how information of our perceived reality is stored in these connections. Just as importantly, we hope to discover how this information is retrieved and processed, parsed, and associated with other memories and senses. Why are smells so often vividly linked with memory?
   
   
8. How did life evolve?
   
   Although this is a question we will never be able to definitively answer (unless Number 18 becomes possible), I think we will one day be able to demonstrate practical ways in which life can evolve from non-life. In 1953, Miller and Urey demonstrated the formation of essential amino acids by simply electrocuting boiled methane, ammonia, hydrogen, and water – compounds believed to be abundant on the early Earth. Since then, many researchers have uncovered many specific conditions that can result in the formation of compounds necessary for life as we know it, including the formation of nucleic acids. It is very conceivable that in the near future, scientists may demonstrate the formation of self-assembling, replicating molecules in such an experiment. Perhaps they will then show how these replicating molecules can acquire membranes, like the phospholipid bilayers of our own cells (which are already known to be self-assembling). A wide variety of theories exist concerning the abiotic origins of life, too many to debate here, and I think that we may in our own lifetimes find practical methods that our own molecular ancestors might have used to become life.
   
   
9. What is the exact evolutionary lineage of all life on Earth?
   
   As above, historical events are by definition inherently unknowable, from a definitive standpoint. However, as the fossil record continues to accumulate, and more importantly, as more and more genomes are sequenced, we will be able to use compare the specific DNA codes of all life on Earth (or as much as we want) to calculate the ultimate Tree of Life on Earth. There will always be holes, and specific areas of fuzziness in the data. Many organisms have been show to transfer genetic material between species, largely due to things like retroviruses and bacteria, which can muddy our understanding of specific lineages. Nonetheless, we will eventually construct a tree of evolution that comes close to outlining the entire history of natural selection on Earth.
   
   
10. Can we engineer our own evolution?
    
    The trajectory of current molecular and developmental biology places us squarely in line to eventually understand the contributions of all genes within human development and physiology. We are already at the point where embryos can be screened for genetic defects, such as Trisomy 21 (Down Syndrome), before being implanted into a woman’s uterus. Our tools for genetic manipulation are improving, though we are still far from using gene therapy as a routine treatment. It seems likely that we will one day be faced with the opportunity to engineer our own evolution. The current state of civilization seems to suggest that at least a macro level, humans are not experiencing selective pressure to evolve, other than negative selection against disease (see my article on human evolution below). However, we may one day be able to direct the course of our own evolution. We would need the currently unimaginable computing power necessary to simulate potential genetic changes, and superb genetic tools. Perhaps with enough knowledge of developmental biology, physiology, anatomy, and with the necessary computing power and tool, we could make our species happier, adapted to undersea life, more intelligent, free of disorder and disease, or any number of things we can imagine for our species. Of course, there are enough moral and societal issue with this possibility to fill a Wikipedia. Then again, who knows what kind of world humans will live in many generations from now.
    
    
11. What is are the costs and benefits to specific changes in the brain?
    
    An interesting issue has been brought up by the fields of clinical psychology and cognitive psychology, and it is the issue of the cost/benefit of deficits or enhancements in the brain. Many have speculated a growing list of artists, geniuses, and creative thinkers from our history to have been autistic, or at least have had personalities on the autistic spectrum. In addition, creativity has been positively linked with bipolar disorder (formerly known as manic depression). The study of neuroscience and neuropsychology will likely discover some interesting links between gaining certain abilities or traits, while displaying deficits of others. We have all heard of the rare “savants." If do get to the point of self-directed evolution or even personal enhancement with drugs, it may be interesting to define the interplay between these different traits in the human psyche.
    
    
12. How does a single cell turn itself into a thinking, breathing organism?
    
    How does a fertilized egg regulate its own genes and control the timing and three dimensional growth of cells to form tissues and organs? The field of developmental biology is currently in an explosion of data. What at first seemed only insanely complex, now seems near-infinitely more so with the discovery of the roles of things such as microRNAs, epigenetics, maternal contribution on development, on top of the role of protein-coding genes. It seems like it will take centuries for us to parse out the different factors, interactors, and processes involved in the construction of an organism. However, time is something we’re not concerned with here. Assuming all remains right with the world, science will almost definitely explain exactly how a sperm and an egg can come together to create someone like you.
    
    
13. Is there a maximum human life span?
    
    The human body did not evolve to be particularly long-lived. As we age, our somatic telomeres shorten (which degrades genes at the end of a chromosome), we accumulate mutations, oxidative damage, and cellular debris, and we develop diseases. How many of these things can we overcome? As of this moment, there is only one proven method of extending life spans in mammals: caloric restriction. Eat less, live longer – at least on a population level. It remains to be seen how long we can extend the human life. Even if we can extend it further, we will have to address issues of quality of life as well. Nevertheless, I have much optimism that science could extend the human life dramatically, given the time and knowledge.
    
    
14. Can we save our planet?
    
    How much power can we wield over mother earth? Will we learn to alter climate? Will we learn to utilize renewable energy? Can we cure hunger? To me, it seems that we may always remain as ants when compared to the larger forces of this planet. I cannot foresee large scale engineered climate change and weather control. Then again, who could have conceived of gene therapy two hundred years ago? I think that science has already provided at least rudimentary answers to both renewable energy and hunger. The main issues with these seem now to be cultural and economic, which I don’t want to get in to here. Bioengineering is almost assured to produce a new revolution in energy production. I predict that we will soon have microbes producing ethanol or other hydrocarbon fuels from cellulosic material. We already have solar technology. And bioengineering is also in the beginning stages of creating more nutritious foods that are easier to grow. These will have negative effects and issues of their own (such as the loss of biodiversity and increased susceptibility to sudden disease), but these are issues that I believe we can overcome.
    
    
15. Can humans survive on other planets?
    
    Scientists have already discovered over 300 extrasolar planets (planets around other stars). Right now, our technology is limited to inferring planets by the wobble their gravity induces on nearby bodies, so most of the discovered planets are enormous Jupiter-like planets. However, mounting evidence suggests that earth-like planets orbiting “habitable” zones, which are areas of proper temperature ranges, may be much more common than initially suggested. Thus, I think it’s easily conceivable that with new detection technologies, we may discover watery earth-like worlds in our own lifetime, or our children’s. Now can we get there?
    
    
16. Is interstellar travel possible?
    
    This would obviously take a revolution in the world of physics. Light seems to be the limit right now. The closest star to Earth is Proxima Centauri at 4.2 light years distant. However, our current technology cannot even hit 0.004% the speed of light. Perhaps we will one day be able to accomplish a more sizeable proportion of the speed of light and reach the nearest star within a lifetime (10 years at about 50% c), though the energy required for such speeds boggles the mind. Science fiction writers and theoretical physicists are always theorizing that there may be loopholes in the way reality actually works. Perhaps we can figure out a way to circumscribe the peed of light conundrum (a wormhole anyone?). Only science will tell.
    
    
17. Are we alone in the Universe?
    
    Will SETI (Search for Extra-Terrestrial Life) one day finally receive that long awaited telephone call? Will the Phoenix lander discover microbes beneath its microscope (albeit very tiny ones)? Will future craft find beings inhabiting the oceans of Europa that make whales look like shrimp? Our own galaxy contains roughly 100 billion (yes – 100 thousand million) stars. In addition, there are about 100 billion galaxies in our observable Universe. That’s 10,000,000,000,000,000,000,000 stars (assuming our galaxy is average). Considering the frequency with which we are discovering new planets, it seems more than possible that many planets are habitable and may harbor life. The question boils down to the likelihood of life making that first step from non-life, which is a complete unknown. But it is a question sure to be at the forefront of human thought and scientific curiosity. Perhaps we are already being visited. Scientific evidence is lacking, but it doesn’t seem so unlikely to be impossible. See the Drake Equation to play with more astronomical number on alien life.
    
    
18. Is the Universe inherently deterministic or is there “true randomness” in nature?
    
    Do steadfast laws underlie quantum physics? At the macro level, all physics seems deterministic; i.e. every action is causally linked and predictable in theory based on the events preceding it. Current quantum theory seems to indicate an inherent randomness in the behavior of quantum particles. Some claim that this is due to an incomplete understanding of nature – that there are hidden variables and even at the quantum level, causality holds true. The question remains: is there “true randomness” inherent in nature at the subatomic levels? I have read that most physicists currently lean toward true randomness. If there is no “true randomness,” then every event in existence was determined by those before it, thus eliminating the possibility of free will. However, if there is randomness, this at least leaves open the possibility of true free will. Obviously, we are edging into philosophy here – and a topic which we could debate for years, no less. Nonetheless, if physicists can reconcile quantum physics with Newtonian physics and relativity, and all the other weird quantum stuff I am light years from understanding, perhaps they may answer the question of the nature of the existence.
    
    
19. What is the maximum carrying capacity of the Earth? Will we enact global population control measures?
    
    Just how many people can live on the Earth? Some would argue that we have already surpassed the carrying capacity, while others believe we have a ways to go. Given current birth rates and ever-expanding life spans, it seems inevitable that we will be forced to enact population controls on a world scale. It is science that will have to tell us exactly what our resources can handle. No doubt, technology can increase our carrying capacity, if utilized properly.
    
    
20. What is the Ultimate fate of our Universe?
    
    Will our observable Universe eventually cease in a frozen motionless entropic heat death? Or will the dark matter and energy pull all matter back into the singularity from which we exploded (The Big Crunch or Gnab Gib? This is still a hotly debated topic. We lack much crucial data. However, current measurements indicate that the Universal expansion is accelerating and not decreasing in its rate of expansion. How much dark matter is actually out there? And…
    
    
21. What is dark energy and dark matter, anyway?
    
    I don’t have much to say about dark matter or dark energy, and I’m not sure that physicists have much more. Actually I’m sure that they do – I am probably just avoiding them. Something seems to be out there, swirling within galaxies, holding them together, and pulling groups of galaxies into clusters and superclusters. We have inferred its existence from its effect on other mass. More than that I cannot tell you. I hope that science will tell us much much more in the coming years.
    
    
22. Is time travel possible?
    
    Yes. Forward at one second per second. I jest. Again, theoretical physicists have come up with scenarios in which some form of time travel might be possible. They all seem baffling to me. I had high hopes for the Time Traveler Convention of 2005, but unfortunately it seems that humans will not eventually discover time travel, or that when they did, they will have never heard of the Convention and so failed to show up.
    
    
23. What is the true nature of existence? Parallel Universes, multiple dimensions, strings?
    
    Physicists – I leave this one to you. I have tried on many occasions to wrap at least a few brain cells around string theory (may those neurons rest in peace). If science ever comes to grips with the nature of our physical reality and devises the Grand Unified Theory of everything, I sure hope the math can be translated into more conceptual terms. If it turns out that we live in only one (or four) of 13 dimensions or some other such craziness, we prove it, and I still cannot understand it, it will be a sad and anticlimactic day.

Well, those are the best questions I have to offer. Again, please feel free to leave your own two cents. I am sure there are worlds of interesting and important scientific questions left to be answered.

Biology Search Engine

Here's something some of my fellow biologists might find useful: http://www.vadlo.com/.

It's a search engine, like Google, but restricted to biology. It seems to work pretty well. Pulls up quite a few protocols and the like. A potentially more useful search category is the ability to search for powerpoint presentations. This could come in handy for biology teachers looking for good slides.

Embryonic Stem Cells Turning Into Brain Cells

These are mouse embryonic stem cells that I coerced to differentiate into brain cells. The neurons are green, red represents the radial glia (they proved a scaffold for the neurons), and the blue are the nuclei of the cells (that houses the DNA).

Hope in the Black Void of the Unknowable

All life and human experience is devoid of meaning. The Universe is nothing more than an enormous cosmic accident. It is an accident that will be corrected in due course, as the Universe and its inhabitants are fated to be destroyed in an equally pointless cataclysm of some kind or another - whether it be through a Universal collapse to a singularity or a dissipation of all energy in an entropic heat death. At least this is the view of our Universe as seen through the eyes of empiricism. Is it really any wonder then that 40-50% of the American public, depending on which poll you’re looking at, prefers the idea of creationism to the theory of evolution? Our morals, our accomplishments, our feelings and thoughts, our connections to others and to the world in which we live – all the things we as a species hold dear – are apparently no more than blips of energy in an inconsequential cosmic blink.

Yet this is the Universe that we face if we look at it only through the lenses of logic and reason. How much blame can we really place on our Earthly brothers and sisters for rejecting such a worldview? No doubt, within certain psyches such a view might inevitably lead to depression, apathy, and a callousness toward humankind and existence. Do we as scientists wish for every other person on this planet to truly see and understand our world through sensory perception and evidential experience alone?

The media is currently awash with the pontifications of atheist personalities such as Richard Dawkins and Christopher Hitchens, both of which claim that faith and religion are the downfall of humanity and the yoke holding us back from true existential accomplishment. According to them, if only people could truly understand the awe and wonder brought forth by an intimate inspection of existence, from the microscopic to the astronomical – if only they could see that faith is unnecessary – the world would reach a new height of enlightenment and elevated existence. I believe their motives are noble, and I find the essence of their arguments to be true – that is until they cross the line of reason into their own forms of faith. For both of these now famous authors have fallen into the pitfalls of their own arrogance. Through one word alone they have both done a disservice to the endeavors of science, while providing fodder for those who wish to remain blind to the forces of nature. The word is “atheism.”

The error is a small one, yet profoundly significant in its effects. Both men claim to be atheists. Their position is that there is no God. There is no evidence for a God and even entertaining the notion of one is foolishness. Perhaps it is. However, neither of them seem to grasp, or at least to express their understanding, that underlying all knowledge and all science is one major faith, one assumption. This is the assumption that our senses and experiences are relating real information about reality. That we are not merely in “The Matrix.” There is simply no philosophical workaround to this argument – it is impossible to absolutely know anything. Thus, even if science can tell us exactly how the Big Bang began, we can never know what if anything came before that moment or whether it was orchestrated by some deistic entity. So by definition, any scientist who claims to shape all of his or her worldviews around empiricism and logic, must declare themselves agnostic: the view that the existence of a God is unknown or unknowable. Or they should at least qualify themselves as “agnostic atheists”, which takes a more probabilistic view claiming that there is no evidence for or against a God, but that the Universe as we know it seems to suggest that there is not one.

I agree with the supposition that all orthodox religions and dogma as we know them are farce. The genesis stories throughout the religious world have been disproven as far as it is possible to do so, given the above inherent unknowability of all knowledge and the limitations of our ability to measure history. Evolution is not even a debate within the world of science. Every month it seems a new “transition fossil” is found to plug another hole in the fossil record. A steady stream of hominid fossils have traced our own evolution back about seven million years, and 85 million years for all primates. The only debates of this are micro-debates about which species begat which. As for the fossil record, one must understand that by its very nature, every time we fill one hole, two more arise on either side of it. Our understanding of molecular biology and genetics has only cemented our theories of evolution and natural selection. Natural evolution is irrefutable, insofar as the above prime assumption is acknowledged. The world is not a paltry six thousand years old. The Earth and the solar system we inhabit all formed about four and a half billion years ago, over nine billion year after the formation of the Universe itself as we know it. Thus, I agree with the self-branded atheists that it is foolishness to believe that a single man and a woman talked to a demonic snake six thousand years ago and bred to yield our current population. This story, along with all other religious dogmas, appear to be nothing more than fables – parables that helped us once cope with and explain our own existence.

But that brings us back to the original question: do we really want all of humanity to live as if our existence is a meaningless accident? It is my view that we in the science community should embrace the idea, from a philosophical standpoint, that there very well may be an unknowable entity – Aristotle’s “unmoved mover” - that crafted the laws of physics as we know them, that set the ball in motion. We can never even attempt to discover what underlies the laws of our system, for we are within the system, a part of the system, are the system. I personally have no problem admitting that this existence is likely as ethereal and meaningless as a flake of dead skin. However I am not so sure that I have faith that the rest of humanity could cope with such a prospect. Perhaps this is arrogance on my part. The evidence, though, seems to support my lack of faith in human mental well-being: how many of the worlds problems and crimes are caused by individuals feeling lost and unimportant in this world?

Thus, I suggest that we push our science, which is everyone’s science, as strongly as we can. We must educate our children about where we as a species come from. We must make them understand that we use science because it is the only proven method of obtaining anything close to actual knowledge about our Universe and existence. However, just as importantly, we must admit where our knowledge cannot reach, and allow that place to be inhabited with hope – a hope that maybe, just maybe, in that dark void of unknowability lies a meaning to our existence, a meaning we can never know or understand. We must make them understand that although the fables passed down from our ancestors are untrue and no longer useful as a defining belief, the true possibilities of our meaning and our worth may be infinitely larger than they ever imagined. I believe that if we take into consideration the grandness of nature, the mind-boggling array of galaxies in our Universe, and the insanely complex biology and chemistry within ourselves, the unknowable creation of our Universe will seem only that much bigger and infinitely more awe-inspiring. As the philosopher Karl Popper once said, “Our knowledge can only be finite, while our ignorance must necessarily be infinite.” It is in this infinite ignorance where our only hope for greater meaning may lie.

The end of evolution? (yes and no - mostly no)

I occasionally hear people talk about what humans will look and be like in the future. They hypothesize about what the next steps in human evolution will be. Will we continue to become more intelligent, taller, or more able to manipulate things with our hands etc., according to the previous trends in our evolution. However, let us really think about this. In our society today (and I'm mainly referring to the developed countries) we have amazing health care and it is fairly certain that our ability to fight and control disease externally through drugs and treatments will only get better. Soon even those with severe genetic diseases that would have eliminated them from the gene pool before adolescence a century ago will now be able to live relatively long lives. Essentially, we no longer have any reproduction of the fittest - everyone is about as able to produce offspring and pass on their genes as everyone else, as a broad generalization with some exceptions. Of course I realize that at a micro-level some evolution will continue to occur. It is not really correct to say that Darwinian evolution no longer applies to human populations. As I said there will still be some survival (and more importantly, reproduction) of the fittest, but only at a micro-level – mostly at the level of eliminating disease. The diseases that completely prevent reproduction (such as down syndrome) will always be weeded out of the gene pool because the down syndrome traits (an extra 21st chromosome) cannot be passed down to the next generation (or they are passed down at a much reduced rate). Also, certain genes may fluctuate in abundance throughout the population due to environmental and cultural factors. For instance the percentage of brown eyes will probably increase in the US as the Hispanic populations increase and disperse their traits through the gene pool (this is just a random possible example that may or may not happen). This process is more akin to genetic drift than to actual trait selection.

Evolutionarily speaking, no new or novel traits that appear will have any reproductive advantage, because everyone is already able to reproduce as much as the next guy, in general. Before long most countries will have mandatory family size limits to control the world's overpopulation. Many people can't see this occurring in the near future, but in a century or two we will have no choice. In the past, one of the main factors leading to evolution was a genetic change allowing individuals to reproduce more children or to reproduce more efficiently, consequently leading to a proliferation of those traits within the gene pool. Assuming only natural selection as the force of evolution, population control will eliminate this selection. No one will produce more offspring, thus no specific traits will be able to propagate faster than any others. Furthermore, since everyone is basically equal in reproduction, we will not "evolve" new and better genes that make us smarter or stronger (such genes would not be selected for and would not propagate through the population). In fact, it seems more likely that we will accumulate more defective genes that arise due to normal DNA replication errors and environmental mutagens and pollutants, and we will simply treat these problems with pharmaceuticals or therapy. Unless these mutations are so bad that they prevent reproduction, they will continue to be passed down.

Of course, you can probably see where this argument is going. This lack of evolution and accumulation of faulty genes will probably not happen. Not only has technology virtually eliminated any natural selection, with a few exceptions, it has created the new prospect of artificial selection. The human race WILL evolve, but it will be according to an actual plan, as opposed to the random forces of natural selection. Alternatively, a culture of breeding only with the most genetically fit might arise, a la “GATTACA,” however we see even today that it is the poorest of the poor and the most uneducated that actually has the highest birth rates (no offense intended to these populations). Honestly, if we want our lineage to continue and evolve (I hesitate to say race - race is too static of a term for a changing species), we have no choice but to actively evolve. Now don't misunderstand me and think that I'm saying we should go ahead now. Far from it! We are still in the infancy of understanding human genetics and development. We are still far from understanding exactly how the brain works and gives us self-consciousness, imagination, creativity, empathy, love, hate, and all the other nuances of human consciousness. However, that doesn't mean that we will not figure it all out eventually. We will, assuming we don't annihilate ourselves first. There are also many ethical problems with this that will have to be resolved within the population and I'm not sure how this is could work, under our current culture. However, we are already seeing the beginnings of this movement in the genetic screening of embryos for implantations. The number one thing that will have to happen is complete public education on the issues, the technologies, and the implications that go with them. Many people feel that there is something inherently wrong and sinful in "playing" God. I can see why some folks would feel that way, but I also believe that many those feelings stem from ignorance of the facts. Assuming we can overcome our fears and our ignorance, we may well be able to evolve consciously and designedly. No one is really in a position to say exactly what traits we will choose to develop - that prospect is still too far off. It certainly will not create a "perfect" human race as many people fear. That term really has no meaning. Imagine, just for fun, the human race actively developing traits that increase the sense of compassion and empathy, increasing our intelligence, giving a population of humans external gills and leathery skin to colonize the other three-quarters of the earth. Of course, these are far out ideas and have a ring of fantasy and science fiction in our ears. But these types of things are conceivably possible in the not-too-distant-future. We are learning more about how organisms develop and how the genes and environment direct this development every day.

Thus, technology hasn't really stripped us of our ability to evolve. It has simply made it so that relatively minor accidental mutations do not have the pressures to give any individuals a better chance of surviving and reproducing. Honestly, which sounds better and safer to you: waiting around for something to damage our DNA in just the right way to confer some sort of survival or reproductive advantage, or actively and carefully designing and developing these mutations and additions in order to further our long-term survival and potential?

Something one must keep in mind is that if any major catastrophe were to occur and cripple our civilization and society as we know it, the old method of natural selection would most likely resume. However, we may even be able to prevent this from occurring using our abilities of genetic manipulation. I can easily foresee us colonizing space, Mars, and, perhaps far in the future, other solar systems (assuming interstellar space travel or suspended animation are ever figured out or even possible). Regardless of how many of these ideas we as a species bring to fruition, you can be guaranteed that the human race is not truly in a state of evolutionary suspended animation, though it may appear so during our short technological adolescence. Remember the time spans involved in Darwinian evolution. If Earth history were compressed into a single year, humans would not have arrived until 2PM on December 31^st. We have not yet even been able to look at ourselves in the mirror long enough to determine if we are really evolving or not.

Science as Dr. Frankenstein

I hope every single one of you realizes that "the perfect human" is a phrase completely devoid of meaning in a constantly changing world and universe.

I read an article yesterday in TIME magazine that made some good points about genetic engineering, and as I often do, I started thinking about this subject: scientists genetically engineering humans to make them supremely intelligent, strong, agile, wicked, purple, hermaphroditic, or a combination of the above. The article was called "Why Pro-lifers are missing the point" and its main argument was that the moral question of stem cell research should not be where the tissue is coming from (dead fetuses vs. embryos for in vitro fertilization), the question should be where it is going?

I think this is a very valid concern and it ought to give us pause to consider the implications of genetic engineering research. However, I’d like to tell you some of the things mentioned in the article that I believe are full of the proverbial “it”.

First,

"In 1998, Massachusetts scientists injected a human nucleus into a cow egg. The resulting embryo, destroyed early, appeared to be producing human protein, but we have no idea what kind of grotesque hybrid entity would come out of such marriage."

What!!?? No "grotesque hybrid" could possibly come from this. Why? Because THERE IS NO COW DNA IN THE EGG, except for some maternal mitochondrial DNA. It was an enucleated egg, replaced with a human nucleus. The only thing that would happen is the embryo would die because there would not be the correct maternal mRNA for proper development. Besides where would the fetus gestate? You gonna keep it in a box?! (Thank you Monty Python) I seriously doubt that you could just stick it in a cow. First, the embryo would not be able to implant into the cow’s uterus. If it miraculously could, the cow's body would more than likely detect a "problem" with the embryo and would reabsorb it or flush it.

Second,

"Last October, the first primate containing genes from another species - a monkey with a jellyfish gene - was born. Monkeys today. Tomorrow humans."

This is true. I've seen pictures of the little rhesus monkey, and damn was he cute. I should note that although his chromosomes contained the green fluorescence protein gene, the gene was not expressed (meaning no protein was made and the gene was essentially just sitting there doing nothing). Yes humans are next. Big deal. Some of our genes were imported from other species into our own genome by retroviruses! What is better, random insertion of a random gene with an astronomically small chance of it helping an organism, or carefully planned and controlled introduction of a gene for a specific beneficial purpose with a much higher chance of success? You make the call.

Finally, the article says,

"but just around the corner lies the logical by-product of such research: the hybrid human-animal species, the partly developed human bodies for use as parts, and other grotesqueries as yet unimagined."

As for the human-animal hybrids, in the not-too-distant-future this may become possible. However there would be very little incentive for this other than the "look what I can do" factor. What is so inherently "grotesque" about a species of organism that has some human and some animal aspects? Any hybrid we created wouldn't be human. Humans are animals, therefore the new hybrid would simply be another species on this planet. God knows we've killed enough off already. I personally think it would be pretty amazing to have another intelligent species on this planet. Besides if people create animals with human intellect, it isn't going to be for food or slavery. It almost seems preposterous to imagine, but I think it will not be so in a few generations.

It is very possible in the future that if animals continue to be exploited by humans for food, the animals will likely by made dumber and stripped of pain perception, which will make slaughter a little more like cutting down a tree.

Some of this technology may even allow us to replace some of the species we’ve already killed off.

Human bodies grown for body parts are not a "by-product" of this research. They are one of the ULTIMATE GOALS of this research. Do you realize how many people die every day because they can't find a heart, lung, liver, or kidney donor? Now imagine if we could grow human bodies with no conscious, self-awareness, feelings, or even the brain structures to allow these things. It wouldn't be a deformed grotesque human, it would be a TISSUE CULTURE for saving lives. This would be revolutionary. Tell me you won't appreciate this in twenty years when your liver is an alcohol-ridden degraded soggy mass full of holes.

People think we're trying to play God and that we are trying to do in a short time what it took nature billions of years to do. But nature is not an entity that sat here and thought "I wonder what would happen if I stuck feathers on that little lizard’s arms?" It took millions of failed mutations that led to grotesque deformities and sudden deaths for every single gene that benefits an organism. If you were to watch evolution through a time-lapse, it would not be a pretty sight (actually I think it would be fascinating and beautiful, but that's just me) compared to what "grotesqueries" we might create.

Now I am not saying we should just start engineering things and cramming different genes in different organisms to see what we can sculpt. Life is not a toy and there are many, many, MANY obstacles to be overcome. We still don't have a single descent way of introducing a gene into a human chromosome in a controlled way as to prevent the disruption of other genes or cause a myriad other problems. All our current techniques involve "shotgun techniques" shooting DNA into a nucleus, hoping the gene gets stuck in a good place on a random chromosome. Most of them involve using viral capsules (basically just containers with no viral DNA) to get the DNA into the cell, which is so far turning out to be very inefficient and unpredictable. This is not how human genetic engineering should be done. But as long as we (which includes everyone in the public) proceed which extreme caution, skepticism of all data and discoveries, and keep an OPEN MIND, then I will remain optimistic of the benefits that genetic engineering and stem cell research can do for our race.

At least the ones that can afford it.