biochemicalsoul.com

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

2008-09-03T13:57:00.010-04:00

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

2008-09-03T13:27:00.003-04:00

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.

Behavioral Mimicry in the Golden Garden Spider

2008-09-02T21:37:00.005-04:00

I witnessed a pretty awesome display today by my friendly neighborhood Golden Garden Spider (Argiope aurantia), that I had never before seen. In fact, I had no idea that spiders would make such defensive displays.

As I approached her web, I noticed the web start to vibrate back and forth in quite an exaggerated fashion. So I ran and grabbed my camera. When I got back out she had stopped, but she started back up immediately as I got close.

Note - my hand is actually about 6 inches from the web. Also, my hand produced no wind (you can see this clearly toward the end of the video - the last ten seconds are by far the best).

Considering the bright yellow and black markings, my nearest guess is that she was mimicking the movement of a carpenter bee or some other poisonous hymenopteran (we have lots of carpenter bees). It seems clear that it was her way of saying "get the fuck away from me! I'm dangerous". Of course, it may be that it's not mimicry at all, but to me it looks very similar to the movement of the carpenter bees against that very same wood as they bob forward and backward.

For another cool picture of an Argiope, see my previous post (which also has some cool black widows from my house).

Call for submissions - Carnival of Evolution #2

2008-09-01T15:38:00.004-04:00

Jason Rosenhouse, the eloquent ScienceBlogs writer over at EvolutionBlog has graciously offered to host the 2nd edition of Carnival of Evolution.

So get those intelligent fingers a tappin' and send your posts to him (deadline for this edition is September 14th). There's a world of evolutionary change out there to discover, and I for one want to know about it.

While you're at it, if you feel so inclined, offer yourselves up in Darwin's name and volunteer to host a future edition.

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

2008-08-31T20:52:00.005-04:00

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 Evolution #1

2008-08-28T21:24:00.000-04:00

Well, I've done it. I've created a new Blog Carnival.

It's called "Carnival of Evolution" and you can find the first edition HERE.

Despite the presence of several really good blog carnivals dealing with science, skepticism, or atheism, which all touch on evolution now and again, there is a dearth of carnivals devoted to evolution (at least I couldn't find any). Thus I think this could fill a much-needed niche.

Now, mine is not a particularly well-read blog, though my traffic has been increasing by the week. My hope is that the purpose and content of this blog carnival will be enough for it to take a life of its own. As such, I now beg any of you with an interest in evolution to host future editions or contribute posts. Spread the word to anyone you know who blogs on evolution, whether from the perspective of the (nonexistent) debate on evolution or on recent science in the field. Hopefully we can get a schedule for it up and running.

I have never hosted or run a blog carnival before, so if anyone has advice I'd be glad to here it.

Democrats, Religion, and Faith-Based Initiatives

2008-08-22T19:47:00.007-04:00

Today in his Pharyngula blog, PZ Myers went off on Democrats for highlighting their commitment to religion and faith and the compassionate accomplishments faith-based groups can make in the world.

Let me first say that in essence, and in principle, I am in complete agreement with PZ. Liberals, progressives, and the Democratic party that we liberals, in general, vote for would serve in an ideal world as the pusher of the rational, scientific, and secular agenda. Instead, what we have seen with Barack Obama is a re-cooption of the Christian and evangelical vote – or at least an attempt to get those voters back – by reemphasizing the Democratic Parties Christian roots.

However, from purely a practical standpoint I think this is the only way we can ever hope to have our government even begin to govern in the progressive way we think it should. Before I expound upon this, I want to mention Obama’s Faith-Based Initiatives plan.

Obama’s Faith-Based Initiatives
When I first heard that Obama wanted to expand Bush’s Faith-based initiatives, I was initially disgusted – for about thirty seconds. The time of disgust was so short because I learned what he really wanted to do. I found out about it by listening to his speech. In it, what he basically says is that the Faith-Based Initiatives were never run properly – they were only a photo-op for Bush to continue to receive evangelical support. Obama, on the other hand wants to rebuild the initiaives. He wants to support compassionate work and community service that these religion-backed organizations claim to want to work for. That’s fine with me for this reason:

“I'm not saying that faith-based groups are an alternative to government or secular nonprofits. And I'm not saying that they're somehow better at lifting people up. What I'm saying is that we all have to work together – Christian and Jew, Hindu and Muslim; believer and non-believer alike – to meet the challenges of the 21st century…

…First, if you get a federal grant, you can't use that grant money to proselytize to the people you help and you can't discriminate against them – or against the people you hire – on the basis of their religion. Second, federal dollars that go directly to churches, temples, and mosques can only be used on secular programs. And we'll also ensure that taxpayer dollars only go to those programs that actually work.”

He’s essentially tearing down the faith-based initiatives and instead building secular-based initiatives, with the religious folks doing the work. Works for me. Personally, I could care less what your beliefs are if your focusing on helping others, regardless of their own faiths. If religion must exist – that’s the direction that I think it needs to focus its efforts. Personally, I think this was a genius move on Obama’s part for the reasons below.

Democratic Christianity
Based on everything I’ve read of Obama, I don’t believe that he is in reality a Christian. Everything about him (except what he actually says on the subject) screams agnostic. But he knows that this is a Christian nation (about 75%). You CANNOT get elected President if you are not Christian or at least deeply religious. So he has spent years crafting his Christian beliefs, developing his Jesus cred. And I’m glad he did.

Only by reclaiming the Christian vote can progressives ever hope to reshape this country. Thus, by highlighting the commitment and accomplishments of the Faithful within the Democratic Party at the Democratic National Convention, the Party may yet recapture those religious votes (or at least a small proportion of them).

Once we get more progressives in place, we can fix this fucked up educational system we have (No Child Left Behind? Don’t even get me started). Only by actually getting rational-minded people into office can we hope to erase the anti-intellectual blanket that has fallen over this country. It may be slow – or it may not happen at all – but you can be guaranteed that the Republican party cares not an ounce about education on true science, intellectualism, and reason.

Thus, the Democrats must, at minimum, act Christian. They must, as Obama has done many many times, proclaim that they have accepted Jesus Christ into a personal relationship. Some may believe it – others may do it for political reasons. But there is no doubt that this is absolutely necessary.

It would be nice to maintain my principles and say “no – we should not put faith and religion on a pedestal – we must not even allow it place within our politics.” But I feel this is naive (Note: I do NOT mean to imply that PZ Myers is naive - we absolutely NEED people like PZ in this world and in this debate - He understands all this much better than I, I'm sure. But he honorably sticks to his principles). Most adults in this country are too indoctrinated to ever be swayed with rhetoric. Most don’t even know what science really is. Consider the fact that somewhere between 50 to 70% of this country believes God had a direct hand in our own creation (depending on the poll), while a reciprocal percentage believes in evolution. Do you really expect that any of these people will vote for a self-proclaimed atheist?

This is obviously not a new argument. Everyone knows (everyone who cares anyway) that every President we’ve had has been Christian (at least in the public eye). Our only hope is to get our people into office by whatever means necessary, and hope we can train the next generation to use their brains properly.

Side Note: Some Christians may read my argument and say "Oh, so Democrats are only fake Christian." To that I would respond that to a large degree, most of the truly Christian Democrats I know walk alot closer to the line Jesus walked than most Republicans I know. Just take our Commander in Chief for example. I don't believe for one femtosecond that he was ever "born again". He, and every other publicly visible Christian in his administration act about as far from the actual teachings of Christ that you can get. How many people have died in Iraq now? Somewhere between 30,000 and 150,000? Oh that's right - according to Gen. Tommy Franks this administration doesn't "do body counts." And it is a well known fact that Karl Rove orchestrated his "brilliant" scheme to get the religious right behind Bush. This is why Democrats should continue with the course they are on with regards to religion. Bush and Rove already proved that Christian voters, by and large, are incredibly gullible.

Really?

You thought Bush was a leader Jesus would vote for?

A Small Example of the Ignorance of (Some) Rednecks

2008-08-22T13:26:00.002-04:00

Today, once again, I witnessed a not-too-uncommon display of ignorance and primitive barbarism in the rural south.

I was driving along a small country back road near my home in North Carolina, listening to a book on CD (no it’s too embarrassing to tell…OK, fine – it was “Twilight” the first novel by Stephenie Meyer about a teenage girl who falls in love with a vampire. Hey screw you – it has amazing character development and who doesn’t like vampire stories?)

Anyway, I was ambling down the road when I saw what I thought might be a snake crossing up ahead. No one was behind me, so I stopped in the middle of the road and got out to check it out. I’m usually the guy who stops to pick up box turtles and carry them across the road – what can I say? I’m a biologist. Sure enough, it was a black rat snake of average length - about 4 feet long – stretched out across the road and moving as if in no hurry. I was glad he had not been run over - usually when I see a snake in the road it’s already dead.

I see a truck pull on to the road a quarter mile down and head right toward us. “Shit,” I think, “This truck will probably aim right toward him.” So I grab the tip of the snake’s tail with the intention of toss him in one quick movement into the ditch. But the snake’s scales were firmly latched onto the blacktop. Plus, he was much quicker than I anticipated. He lashed out at me and coiled into a raised striking position in the middle of the road. He did not find my actions quite as altruistic as I did. Black rat snake bites can be quite painful, considering their row of tiny sharp teeth. I’ve been bitten by one before. They also have a tendency to chew on you once they grab hold. So I backed off.

The truck was not slowing down and other cars were now moving towards us. My car was parked in the middle of the road. I could not see any sticks or anything to handle the snake with, so I decided to leave it to the fates. Maybe the redneck will see that I was just out looking at the snake and will leave it alone, just for my sake (note: I come from a long line of Arkansas/Texas rednecks myself). I get in my car and quickly start it up. I slowly pull forward, and the truck, which had a long trailer attached to the back pulled to a stop in front of the snake. I watched an elderly man get out of the pickup in my rearview. He glanced at the snake, jumped back into the cab, swerved his wheels into the center of the lane, and squashed the snake.

I saw it writhing over itself - dying - as the truck righted into the lane.

The black rat snake is non-venomous. It feeds almost solely, as its name implies, on rodents. The land around where we had been is all farmland, the truck was carrying farm equipment, and the man looked himself to be a local farmer.

Yet this old man went out of his way to smash a creature that spends its days protecting the man’s crops, or his neighbors. Out here, I’ve seen people swerve to hit opossums, raccoons, snakes, and any other little non-dog-or-cat species.

It makes me sick. I simply cannot understand the mind that would derive pleasure from brutally snuffing out our animal neighbors, particularly considering that these are people that have been raised in their presence. I’m not a hippie PETA activist. And I’m not a vegetarian. In fact, I do experiments on animals for brain research. But the pointless, barbaric smashing of animals with a car for pure fun simply reinforces my own views about large swaths of the human population – namely that in many people, pure barbarism lingers within their psyches, reinforced by superstition, fears of things they don’t understand, and utter unadulterated ignorance.

Carnival of the Godless #98

2008-08-17T17:45:00.004-04:00

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.

Building a Better Human

2008-08-15T20:11:00.006-04:00

Transhumanism, to quote Wikipedia is

“a term often used as a synonym for "human enhancement", is an international, intellectual and cultural movement supporting the use of science and technology to enhance human mental and physical abilities and aptitudes, and overcome what it regards as undesirable and unnecessary aspects of the human condition, such as disability, suffering, disease, aging, and involuntary death.”

I often think about the eugenic possibilities of applied science (technology) that may arise in the coming years, decades, and longer. I have long considered myself a transhumanist. That is, I see no general philosophical or moral issues with human enhancement or even directed human evolution, in theory. In practice, however, I think there are several issues that may well prevent our race from ever even attempting such a project. (Don't even think about mentioning the Nazis to me. Though using a warped eugenics, they were NOT transhumanistic.)

Let me first state that I think that external technological enhancement is already in early bloom and will continue to be used to ever increasing degrees. By “external” I mean the use of robotics, artificial limbs and organs, cognitive enhancement, or extension of the senses. However, there is a fundamental difference between this type of enhancement verses the actual altering of the human genetic code and inherent function of human biology.This article will focus almost exclusively on biological modifications.

The moral, social, cultural, and philosophical implications of biological transhumanism have been discussed ad nauseum by many thinkers much greater than I. Books have been written (e.g. Brave New World). Movies have been made (e.g. GATTACA). However, it is only now that we are truly entering an era in which it can be discussed and contemplated from a practical standpoint, and in which we may even begin to realize the transhumanist goals. Not only have we now sequenced the entire human genome, but we are developing tools for altering the genetic code in living human beings. (see question 10 from my previous post: 23 Things Science Can Tell Us about Life, the Universe, and Everything)

However, one thing that I find sorely lacking in most discussions of how we might enhance the human condition is a discussion of Developmental Biology. Before we tackle the main question at hand, I feel I must first take a short diversion into describing development.

Most of the public have heard our genomes described as “the DNA blueprint” of humankind. As any developmental biologist will tell you, DNA is not a blueprint for anything – this is a horrible metaphor for DNA’s true function. The closest metaphor we have for the relationship between DNA and a thinking, breathing human is the relationship between a recipe and a cake. DNA does not describe anything about what a human looks like or how it works. There is not a gene that contains the information on how to make an eye, for example, or what the eye looks like or works. All it tells you is which protein to make at which time and in which cell.

As the field of development now knows, the genes encode for RNAs that encode for proteins (vast oversimplification, but lets keep it manageable). In a single fertilized egg, there are an unknown hundreds or thousands of genes and proteins “turned on” and interacting with each other and with the cell, and even with the mother (in the case of humans).

As the cell divides, new genes are turned on, others are turned off, and a new level of complexity is added. The cells now exist in a growing, changing, dynamic network. This network includes genes, RNAs, proteins, different cells talking to each other, groups of these molecules forming modular, yet interdependent pathways, and all of these interactions are now occurring in discrete areas of space and time.

Yet at the reductionist level, all of these things work by more-or-less simple rules about their own behavior. For example, gene A is only turned on when protein B is present. Protein B is only present in cell type C. So in cell type C, gene A is turned on, to make Protein D. Based on its particular shape, Protein D can only interact with Proteins E and F…etc.

This is another vast oversimplification, and one can imagine this network growing to nearly unimaginable complexity, with some proteins turning genes on, others making stuff like muscle, others making neurotransmitters, and a million other effects ensuing. To go back to our eye example, all of these interactions result in subsets of cells growing and shaping themselves into the structure of the eye at specific times and places. The environment around the eye tells the cells where to go and what to become. Some cells produce tons of beta-crystallin and make the lens. Others grow long axons and connect to the brain, while also producing molecules that react to light. We currently know of about 200 distinct cell types that arise from these interactions of genes, proteins, and cells in space and time.

So, given all this amazing complexity, will we ever reach a point at which we can enhance or evolve ourselves? My own answer is: theoretically, yes – practically, no. (again - see Question 10 of 23 Things Science Can Tell Us about Life, the Universe, and Everything).

There is no doubt that we will eventually have all the pieces of the puzzle of our own development (assuming we last long enough). But there is one key element glossed over in discussions of how we apply our scientific knowledge to human enhancement: experimentation and research on developing embryos. I think that regardless of how much data and understanding we obtain from animal studies and studies of human disease and genetics, we will never be able to apply any directed changes without experimentation on humans. This is a simple fact.

Let’s look at one example: animal cloning. Animal cloning involves the relatively simple activities of inserting a nucleus from one animal cell into the cell of another, and coercing that cell to become an animal. We now do this all the time. Heard about Booger the cloned puppies from Korea yet? But there is one problem – in order for us to get to this advanced (and retardedly stupid) point of being able to clone a long lost and beloved dog, we had to go through the production of thousands of utterly deformed animals of many different species (remember the breast-gland derived sheep, Dolly?). I once went to a great seminar by Dr. Ian Wilmut (the Scottish scientist who cloned Dolly). He showed us some data from some mouse or other rodent cloning he was doing – I don’t remember the specifics. But I do remember that out of something like 500 animals produces, only a fraction were viable.

So I ask, does anyone really think that we can alter human development without going through similar experimental growing pains? How many seriously deformed or deficient human embryos will need to be produced before we get it right? No matter what kind of fundamental change one wishes to accomplish in an adult human body, that change will have to occur at the developmental level, altering specific developmental pathways in specific cells. No matter how big the "cloud" of data, or how vast our computing power, we will always have to test any technique to make sure it works (despite the fact that some actually think that astronomical amounts of data make science unnecessary).

My guess is that such evolutionary enhancements would cause be far too many deformed babies for any even half-moral or ethical people to allow. There are people right now attempting to clone humans, and even this is morally reprehensible. Why? Despite the fact that I have no God, no absolute or cosmologically meaningful morals, I still have an in built belief that conscious-human destruction or harm is wrong. It is hardwired in humanity to place value on human life (with some exceptions and gray areas). Furthermore, there are no positive benefits of human cloning for reproduction, other than scientific knowledge itself, and it will unarguably cause deleterious effects on an unknown fraction of embryos, leading to suffering. And it will most certainly NOT bring loved ones back, though apparently there are thousands of gullible pet-owners who believe otherwise. But I digress. Granted, we may come very very - tantalizingly - close to achieving directed enhancement through work in animals, in human cell culture and tissue culture, but this will not quite be enough.

In essence, I think it is near impossible that we will be able to progress to a point where we can actual tinker with our own genomes (at least during or before developmental stages), due solely to cultural/ethical issues, though it will be technically possible. We will definitely attempt to change adult cells (e.g. gene therapy to give certain cells the ability to produce insulin, which is already underway), but this is a far cry from the types of changes to consciously evolve our form and function – a far cry from adding, subtracting, or changing pieces within the insanely complex developmental pathways that lead to our construction.

Despite my pessimism, there is one possible work around that I can foresee. It will take at least one mad scientist working in conditions that would never be considered ethical today, but it is at least conceivable. Imagine the creation of a human being without a brain – without a consciousness. This is, in fact, one goal of Regenerative Medicine today, though not explicitly stated. We will eventually at least be able to produce organs outside of the body – to grow them in a dish. Now if we had an entire human body devoid of a brain, one could easily see us performing experiments on such a life form without worrying about pain and suffering. (Note: I am ignoring moral qualms from anyone who believes in a soul, or believes that we are “as we were meant to be,” or anyone who thinks that the word “natural” actually means something). But for us to create such an entity, this will likely involve ethically questionable research on humans as well, and it may not even be possible to develop a human without a brain while maintaining the integrity of all other organs. Nonetheless, such a creature could at least give us a “model organism” on which to test our various enhancement techniques. Of course, none of these enhancements would involve cognitive function enhancement, for obvious reasons.

All of this type of research, should it ever occur in any form, will require a progressive revolution in the populace at large. We will have to overcome our archaic “playing God” ideas – (honestly, in what ways have we NOT been trying to play God since the discovery of fire, and the domestification of plants and animals). We will have to get over this idea that somehow “natural” things are better than “unnatural” - the words have no meaning in reality. Accepting genetically-modified foods - a potential savior to world poverty, though it is admittedly rife with its own inherent issues that WILL be addressed - will be a necessary first step. It will also require computing power many magnitudes greater than what we have now, but I think this will inevitably come.

In summary, I have very little faith that our society and culture will allow such enhancements, despite the fact that this is the only way we will evolve, barring major cataclysm. I also think side-effects such as the class divisions between altered people seen in GATTACA, might prove to be too big of an issue. I’m not sure human nature will ever progress beyond dividing itself on whatever divisions are possible. Perhaps if we changed our brains…ahh Catch-22.

Then again, I am but a product of today. Who knows what cultural and societal changes may come? Perhaps our children, or great, great…grandchildren will embrace transhumanism.

I doubt it. As I’ve said before, multiple times, humans are no longer evolving at a macro scale, regardless of what cultural norms envelop us. I think that our animal natures will always grow to repress any escape we might attempt from them.

I hope not.

I really want my baby to have gills.

Flying Spaghetti Monster

2008-08-14T09:39:00.002-04:00

3D animation of the Flying Spaghetti Monster. This is a render that I modeled and animated in two nights. Bathe in the glory of his Noodly Appendages.

Created with the opensource Blender and the GIMP, and Adobe After Effects.

For you CG animators out there, I am providing the .blend file here. Do whatever you wish with it.

If you'll look in my sidebar, I also created a small animated GIF of the Flying Spaghetti Monster. You may also snag this file. Here's the same GIF but with a white background. And here's a GIF on a black background. If anyone wants a version matched to a particular background color, I can make you one - no problem. Let me know if you want the movie itself or higher quality versions.

93rd Skeptic's Circle!

2008-08-13T14:44:00.002-04:00

For those of you who have yet to partake in the skeptical arts, check out the latest edition of the 93rd Skeptic’s Circle Blog Carnival, by City of Skeptics, who hosted the latest edition using a clever ironic Tarot reading (with the final card shown here).

My own most recent post about the second coming of an alien Jesus was graciously included in this edition.

If any of you have your own Skeptical Writings, consider submitting them to the Skeptic’s Circle. The 94^th edition will be hosted by Reduce to Common Sense. Go here for submission guidelines.

The Second Coming

2008-08-12T21:13:00.011-04:00

“Hail, Earthen brothers and sisters, children of the Universal creator. As promised to you millennia ago, I come to you again to bring you unto the Heavens.”

The man raised his hands outward toward the gathered masses, the red scars still visible upon his wrists. The throngs cheered in unison as a great wave of pent up emotion burst forth. The man watched as several humans flailed about as if possessed by ecstasy; several people swooned almost immediately, falling to the ground as their bodies disappeared beneath the assembled flesh. Bulbs flashed a thousand per second. Towering cameras aimed toward the mythical man now here in flesh, recording every word as he spoke and broadcasting the words at light speed across the globe.

Yes, he thought, this will surely go much better than before. Perhaps they are ready.

It had only been a month since he had last laid eyes upon these primate-descended creatures; for them, however, over two-thousand years had past, owing to the unintuitive laws that Einstein had laid out almost a century before. The man swept an olive-skinned hand across his forehead. He still felt the itch from where the thorns had penetrated his scalp. That had been no minor annoyance, but at least they had not left indelible marks.

Their ancestors were so young then. On the cusp of civility and enlightenment, yet still so far. They had most definitely not been ready then. They understood much too little of their own places in existence.

Now, he saw that they had glimpsed this great Universe. They had created primitive ships and had even begun to explore their own cosmic backyard. They must now understand. How could they not?

He beckoned the crowd to still itself – to listen. Silence fell at once as if a muffling blanket a mile on each side had been draped over the world. He could almost sense the hushed anticipation lying on the other side of their primitive broadcasting devices.

The fate of so many rests upon my shoulders. Universe, grant me the wisdom to judge them wisely, as others once judged us.

He ran his dark hand through short black curls. His scalp felt loose, though he had been assured that it would hold. He took a deep breath of the thick air and felt a wave of giddiness sweep through his mind. Luckily, the drugs took effect within moments, rendering the foreign gases breathable.

A tall man in the front let loose a screaming exultation, no longer able to contain himself. “Praise the Lord Jesus Christ, Messiah to mankind!”

A chorus erupted behind the man’s word, punctuated with a blur of similar epithets.

So they now call me Jesus? It is a good a name - as good as any, I suppose. However, their cries both joyous and fervent seeded a deep unease within him, though he knew not why.

He raised his hands once more, and the thunderous cries died as quickly as the first time. “Humankind,” he called, “no doubt you are all keenly aware of the brink upon which you now stand.”

He smiled at the grandiosity of his own words. Though he was not in it for the glory, the adoration for a savior always felt comforting within his ears.

A woman suddenly shouted, “Cast the wicked into Hell! Burn the non-believers and place us at your right hand, Lord!”

Cast the wicked? He balked, his train of thought abruptly thrown. Surely they do not think…no. They must have changed more than this.

The man they now called Jesus cleared his throat before the microphone. “Heed my words, for I am not here to condemn any of your kind.” His deep voice rumbled through the loudspeakers, as an unsteady murmur pulsed through the mass. “As you have now seen with your own eyes, gazing upon this great Universe, your time upon this planet is inherently finite. However, you are not alone in your mortality. All beings must by their very nature be ephemeral. But you have not yet reached the limits of your existential potential. Thus do I come to some of you as a vessel to a new world, as another once came to my people eons ago.”

Cries of disbelief and anger erupted all around. Someone close to the microphone at the front of the stage shouted.

“He is not Christ! He is a false God.”

More shouting sprang from a multitude of human lungs.

“What do you mean ‘your people’?”

“Where is our judgment?”

“Burn the wicked!”

His unease turned to cold fear. Perhaps I have arrived too soon after all. He had seen a crowd of humans turn into a mob once before, and the prospects of going through that again were more than a little unsettling. Unseen by the people below, he tapped a quick pattern on a small device inside his robe in preparation for a quick exit, if necessary.

“Wait,” he cried, “I believe that there has been a miscommunication.” He pointed at the front of the crowd toward the most vocal of the people near the stage. “You – in the red shirt – you have questions?”

The man swung his head from side to side before double-checking the color of his shirt.

“I…yes,” he said, almost inaudibly. He straightened his back and called, “Who exactly do you mean by ‘your people’?”

Jesus was taken aback. What exactly do they think I am?

“Well…my species, of course. We are a race of intelligent beings, not so unlike yourselves. We once stood as you do now, on the cusp between true enlightenment and utter destruction. But also like you, we could not overcome our adolescence alone. We were saved by others.”

The cries of discontent grew to a roar. Jesus shouted into the microphone.

“Please, listen. As I have said, and as promised to your kind two-thousand years ago, I am here to save your race. I bring knowledge, wisdom, and a path to the stars.”

More questions and exclamations drowned the air. He could no longer hear any of them. He gestured for the red-shirted man to join him onstage.

Jesus asked, “Who or what exactly do you think I am?”

The man ambled up the stairs and stared at the crowd, fumbling a hat in his hand.

“We…er…we think – or thought – that you were Jesus Christ, here to deliver the faithful immortal souls into Heaven – into the presence of God.”

Oh no. This is much worse than I thought. Jesus stepped in front of the microphone. “I do not understand what you mean. Why do you still think that you are immortal?”

The man pushed himself before the microphone, much more forcefully this time. “You said so yourself. In the Holy Bible. You were crucified for our sins and your soul ascended into Heaven with the promise to return.”

Jesus bent his head toward the microphone. “What is this Bible of which you speak?”

The man pulled a small, warped New Testament from his back pocket and handed it to Jesus. Jesus held it before him and quickly flipped through it, his hands blurring before the man. Jesus nodded to himself with full understanding. He breathed deeply, growing light-headed, and he waited for his mind to return once more.

“Listen,” he said, taking the microphone in hand, “this book – it is mostly lies and distortions. I did not die for your ‘sins’ as a part of some cosmic plan. Your ancestors were brutal, gullible sheep. They almost killed me, but not quite. I do not fully blame them, for they were but still animals, or near enough. I barely managed to escape. ”

The man yanked the Bible from Jesus’ hand and leapt from the stage wearing a look of utter disgust and disappointment. But the crowd was now beyond calming. Far in the back, waves of force pushed against the flock as those in the rear began to clamor forward. At feeling the wave behind them, those in the front began to grown bold, shouting at one another. Jesus could not tell what exactly they were saying, but it mattered not – he had seen it all before.

“Very well, humankind. I see that you still have a ways to go before you will accept the realities of your own existence. I think I shall now take my leave and putter around the galaxy for a few more weeks. Despite my treatment, I promise yet again that I shall return to you in another millennia or two. Farewell, humans. And heed my plea – use your senses and intellect – and for galactic sakes, stop believing everything you read.”

Without another word, he reached into his robe and pressed a button. A beam of golden light shot from the cloud high above and his body began to rise. The throngs watched as his body disappeared into the Heavens, never to be seen by them again.

Hilarious Conversation with E.T.

2008-08-10T18:48:00.004-04:00

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?

2008-08-10T16:34:00.003-04:00

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

2008-08-08T12:45:00.002-04:00

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

2008-08-07T18:13:00.000-04:00

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

2008-08-07T14:28:00.005-04:00

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

2008-08-06T21:28:00.005-04:00

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

2008-08-05T23:22:00.018-04:00

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.

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.
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.
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.
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.
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)?
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?
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?
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.
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.
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.
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.
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.
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.
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.
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?
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.
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.
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.
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.
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…
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.
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.
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.

NPR This I Believe: Hope in the Black Void of the Unknowable

2008-08-05T17:57:00.004-04:00

Recently, I wrote an essay for This I Believe, an NPR radio series that asks Americans to answer this simple question. My essay has not yet been reviewed; however I doubt my chances of getting selected on the radio program. It is a bit too impersonal, too “what I don’t believe,” and not nearly as eloquent as many of the best essays (for the absolute best – see below mine). My essay is actually a shorter and reworked version of another essay I wrote on the same subject.

Note: If you find that you believe in something strongly and have a story to tell around that belief, I highly recommend you submit your own essay to NPR This I Believe.

This I Believe: Hope in the Black Void of the Unknowable

As a scientist studying the development of the brain and as a student of all scientific knowledge, I find it highly probable that all life and human experience is devoid of inherent meaning or purpose. The Universe seems nothing more than an enormous cosmic accident – an accident that will be corrected in due course as the Universe and its inhabitants are eventually destroyed in an equally pointless cataclysm. At least this is the view of my Universe as seen through the eyes of empiricism, the only eyes through which I know how to look. My morals, my accomplishments, my feelings and thoughts, and my connections to others and to the world in which I live are apparently no more than blips of energy in an inconsequential cosmic blink. However, underlying all of my knowledge and all of science I hold one major faith, one prime assumption. This is the assumption that my senses and experiences are relating real information about reality. That I am not merely in “The Matrix.” There is simply no philosophical workaround to this argument – it is impossible for me to absolutely know anything.

Thus, I cannot conclude anything definitively about my ultimate creator. I cannot absolutely believe in anything. I can only think from within the pragmatic view of science – that my senses work and my experiences along with the collected experiences of my brethren explain my reality better than any other means of purported knowledge. I can only decide to educate my future children about where we as a species come from, though I cannot guess where we may be going. I must make them understand that our science, our knowledge, is the closest thing to an explanation of our Universe we will likely ever have. However, just as importantly, I must admit where this knowledge can never 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 my existence, a meaning I can never know or comprehend.

I must make them understand that although the fables passed down from our ancestors are no longer useful as a defining belief, the true possibilities of our meaning and our worth may be infinitely larger than I 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. I have seen but a glimpse of this awe in the intricate networks of neurons speaking to each other in unintelligible chemical languages, and I can almost fathom an entity setting it all in motion with a mere equation. Almost.

As the philosopher Karl Popper once said, “Our knowledge can only be finite, while our ignorance must necessarily be infinite.” I believe that it is in this infinite ignorance where my only hope for greater cosmic meaning may lie.

The Best "This I Believe" Essay Ever:

NPR This I Believe: I Am Evolution
by Holly Dunsworth, a physical anthropologist at Penn State

I believe evolution. It's easy. It's my life. I'm a paleoanthropologist. I study fossils of humans, apes and monkeys, and I teach college students about their place in nature.

Of course I believe evolution.

But that is different from believing in evolution.

To believe in something takes faith, trust, effort, strength. I need none of these things to believe evolution. It just is. My health is better because of medical research based on evolution. My genetic code is practically the same as a chimpanzee's. My bipedal feet walk on an earth full of fossil missing links. And when my feet tire, those fossils fuel my car.

To believe in something also implies hope. Hope of happiness, reward, forgiveness, eternal life. There is no hope wrapped up in my belief. Unless you count the hope that one day I'll discover the most beautifully complete fossil human skeleton ever found, with a label attached saying exactly what species it belonged to, what food it ate, how much it hunted, if it could speak, if it could laugh, if it could love and if it could throw a curveball. But this fantasy is not why I believe evolution — as if evolution is something I hope comes true.

After all the backyard bone collecting I did as a child, I managed to carve out a career where I get to ask the ultimate question on a daily basis: "Where did I come from and how?"

If our beliefs are important enough, we live our lives in service to them. That's how I feel about evolution. My role as a female Homo sapiens is to return each summer to Kenya, dig up fossils, and piece together our evolutionary history. Scanning the ground for weeks, hoping to find a single molar, or gouging out the side of a hill, one bucket of dirt at a time, I'm always in search of answers to questions shared by the whole human species. The experience deepens my understanding not just about what drives my life, but all our lives, where we came from. And the deeper I go, the more I understand that everything is connected. A bullfrog to a gorilla, a hummingbird to me, to you.

My belief is not immutable. It is constantly evolving with accumulating evidence, new knowledge and breakthrough discoveries. For example, within my lifetime, our history has expanded from being rooted 3 million years ago with the famous Lucy skeleton, to actually beginning over 6 million years ago with a cranium from Chad. The metamorphic nature of my belief is not at all like a traditional religious one; it's more like seeing is believing.

So I believe evolution.

I feel it. I breathe it. I listen to evolution, I observe it and I do evolution. I write, study, analyze, scrutinize and collect evolution. I am evolution.

Amazing, no? If you enjoyed this beautiful and poignant essay, I highly recommend you read the interview with Holly Dunsworth on the excellent Forms Most Beautiful blog (one of my favorite blogs on the internets).

Spiders and Insects Around the House

2008-08-04T19:42:00.006-04:00

First, for the last two summers my property has been overrun by the Northern Black Widow (Latrodectus variolus). These are distinguishable from the Southern Black Widow (Latrodectus mactans) by the fact that Northern Widows have broken hourglasses on their abdomen, while Southern widows have complete hourglasses. Note the broken hourglass on the female below.

Next up, we have the Yellow Garden Spider (Argiope aurantia), or I used to call them when I was a kid: the "zig-zag spider", for obvious reasons. I love it when I get these around the house. They're just plain cool. I also have an amazing video of the female below spinning her egg case.

These are freaky little creatures: I believe they are Coreidae sp. That's about all I can figure out with a quick look on bug guide.
Menacing Giant Stag Beetle (Lucanus elaphus). These things scare the crap out of my wife.

And finally, an awesome example of obvious Natural Selection: a moth of the Hydriomena genus.

Biology Search Engine

2008-08-04T19:07:00.003-04:00

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.

Neuroscience Disproves The "Self"-Containing Soul

2008-08-04T15:15:00.003-04:00

Most people who believe in the presence of a soul, also believe that that soul contains some sort of information about who “you” are. They believe that it contains some essence of your self, your memories, your personality.

However, there now exists within the realms of neuroscience, a plenitude of evidence that such a soul does not – cannot – exist.

Claim 1: My soul contains the essence of my core personality.

Evidence against it: This one is quite simple. All we have to do to see that this is unlikely is look at brain injury patients. It is irrefutable fact that brain injury can lead to profound changes in personality. Therefore, if one’s personality can be fundamentally changed by brain injury, then one must argue that if a soul exists and contains your personality, then it is also damaged by brain injury. The corollary to this is that if your brain is destroyed, then the soul that contains your personality is also destroyed.

Claim 2: When I die, my soul retains my memories.

Evidence against it: Similarly, many many things can kill the cells (and their network of synaptic connections) that store your memories. Alcohol and substance abuse, brain trauma, etc. Furthermore, there are mountains of evidence that your memories are not static, that they can be changed by suggestion, or changed by time. We have all experienced change of our own memories over time, whether by repetition of embellished stories or simply by memory loss. Our memories lie solely in the physical makeup of the cells in which they are stored, much like digital data on a hard drive (though our own memory storage is much more complex and still being deciphered). Essentially the same argument as above indicates that if a soul exists, it cannot contain our memories, or alternatively, when memories are lost, so too are those parts of the soul.

More Evidence: Everything about what makes “you” you comes from an entire life’s worth of experiences – smells, laughs, people, conversations, traumatic events, feelings, etc. These are all incorporated into your memories, and they help determine your personality. You are not born exactly as you exist today. Your neural pathways, your memories, your reactions, and your emotions are all developed over time, and encoded into the unimaginably complex connections within the 100 thousand million neurons in your brain. Injury can change or erase all of this. Thus, again, if your personality and memory changes, so must the thing which holds them. If your memories and personality die, then so does that which defines them.

All of this does not and cannot rule out the possibility of the existence of some other definition of the soul. But one must wonder: if the soul does not contain my memories, personality or any other characteristics that define my “self”, then in what capacity can I say that any immortal soul is really “me”? Even if your soul lives forever, “you” as you define yourself will be as nonexistent as the brain structures that held “you.”

If brain injury could only delete parts of your personality or delete memories instead of actually changing them, then one might argue that the brain has merely lost access to those parts of the soul – that those parts of “you” are still in there. But the fact that both can be changed suggests that the soul either does not exist, or that it is changed in the same way that the personality or memories are.

It seems that modern neuroscience suggests that any “soul” we contain has no real meaning in regards to containing the “self” as we define it. Thus, any immortal soul we may contain is about as significant as the immortal matter of which we consist. Sure, my energy and atoms might remain for all eternity, but is that “me?”

No.

Embryonic Stem Cells Turning Into Brain Cells

2008-08-03T16:13:00.005-04:00

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).