Why do humans care for their disabled children?

I recently came across an article in Discover magazine that talks about the discovery a fossil a disabled child half million years old that was cared for and nurtured for 10 years.  You can find the article here:
The fossil is 530,000 years old and belongs to the species Homo heidelbergensis.  It is a 10 year old child with a birth defect that would have caused severe mental and physical handicaps.  The fact that the child lived for 10 years is strong evidence that we developed the will and capacity to care for severely disabled offspring long before we became fully human.  Such behavior of course is not evolutionarily adaptive.  In fact, the effort that must have been exerted to care for this child who would no doubt have no chance of producing offspring of his own, would have had to be much greater than the effort required for the care of a child without such impairments.  This effort must have extended to the tribe not just to the mother.
In evolutionary biology, a trait is adaptive if it is heritable and it bolsters reproductive success.  The fact that caring for a disabled child is not adaptive means that it is truly a selfless act. 
This article struck a personal note for me because I have a 9 year old little boy with severe mental and physical disabilities.  How is it that my love for my children is equal when from an evolutionary perspective, one might assume that I should invest all of my resources into the child with the potential of passing on my genes?  Am I just conforming to some cultural norm?  Boyd and Richerson (see my paper on cultural evolution in my culture evolves post below) talk about an arms race between cultural and biological evolution.  The capacity for culture on balance is adaptive and improves the individual's chances of survival and passing on their genes.  However, every adaptive trait has some kind of a compromise involved because evolution cannot produce perfect solutions to problems.  Culture is an extreme example of this.  Our capacity for culture, allows us to escape the tyrannical demands of our selfish biological interests.  Because of culture, we are not necessarily chained to the demands of reproduction and survival.
A cultural explanation may be part of what's going on but cannot be the whole answer.  Clearly, 530,000 years ago there were no organized religions guilting this tribe into caring for their disabled members.  In fact, the child was probably a burden to the rest of the tribe so it is doubtful that the parents would have been judged harshly for choosing to abandon the child. So, it seems to me that these parents did what they did purely out of love.
Even in  many modern cultures, having a disabled child may be looked down upon as a shameful thing.  This may compel some parents to abandon their child at an institution and keep the whole thing a secret.  Nevertheless, there are many examples of parents raising their disabled children even when they are looked down upon and shamed by their culture (I need to do some research to get some clear examples of this.)  So, cultural conformity is not the explanation.  Despite being maladaptive I believe there is a strong biological tendency for parents to care for their disabled children.  Parents that make these sacrifices do so out of love, and not necessarily because of cultural conformity.
If this is true, then how did such a tendency that transcends cultures escape the tyrannical hatchet of natural selection?  I believe that the answer may be connected to the uniquely human trait of caring for our elderly.  Such care is biologically adaptive.  Tribal elders were a vast resource for vital knowledge in ancient societies.  Tribes that cared for their elderly eventually out-competed those that didn't.  We learned to have compassion for and to take care of those who could not care for themselves.  Care for the elderly has clear biological advantages that have been selected for.  Is it possible that the same cultural mechanisms that evolved to care for our elderly are the same ones that compel us to love our children unconditionally and to experience love in its purest form?

Bioinformatics and scientific workflows

This semester I am working with a fellow research student to develop some workflows to automate some analyses for my bioinformatics professor.  This week I have been evaluating a scientific workflow solution called Taverna.  I have been learning the basics from a powerpoint presentation here. 
Taverna allows the user to construct workflows from pre-existing modules that do everything from retrieving sequences in genbank to aligning, analyzing and displaying the data in graph form.  This is definitely a fully featured workflow solution.  Workflows can be configured to be fail-safe, meaning I can specify alternate modules if 1 is not presently available.  Also, when specifying more than 1 input, for example 4 gene sequences instead of 1, Taverna will automatically iterate over each input.
Our next task will be to discover if our workflow problem can be solved by configuring Taverna workflow with modules that already exist.  I would actually like to use the API to create my own modules.  Also, we need to investigate how easy it is take advantage of multiple processors and machines.

Mitochondria and the meaning of life

I stated in my last post that it would be impossible for bacteria to evolve eukaryote-like complexity without symbiosis because trim genomes and small size are selected for.  The size of bacteria is constrained because they need a high surface area to volume ratio in order to respire.  But, some bacteria have found ways to increase surface area by changing shape or with infolded membranes.  We know that this path has never led to complexity over 4 billion years of evolution, but why? 
Lane believes that it is because as energy generation becomes larger and more complex, local control is essential.  We all know that mitochondria have their own genome.  Over time, mitochondrial genes have migrated to the nucleus.  The exact genes that have migrated are different in different species but there is no species that has lost all mitochondrial genes.  The ones that are retained generally benefit local energy production regulation.  There are many disadvantages to retaining genes in the mitochondria.  They evolve about 20 times faster than nuclear genes as they are more susceptible to mutation.  Also, the genetic machinery must be maintained in each of the hundreds of mitochondria in each cell.  Since we know that there is not even 1 example of a eukaryote losing all of its mitochondrial genes, there must be a huge advantage to these genetic outposts.  Lane argues that local control is absolutely essential.  If mitochondria didn't have their own genomes, they would not be able to individually regulate energy production.  Regulating hundreds of mitochondria from the nucleus would be extremely complex and it may not be possible for such a mechanism to evolve.  This is the problem with bacteria with infolded membranes.  If they were to grow and become more complex, localized control of energy production would be essential but there is no mechanism for such a structure to evolve.  Symbiosis got around this problem.  That is why eukaryotes alone broke free of their bacterial chains!

Why are bacteria eternally simple?

This question is explored in Nick Lane's book Power, Sex, Suicide.  Eukaryotes are indeed unusual.  They alone have ascended above the simple constraints of bacterial life. 
Bacteria remain simple because natural selection keeps them simple.  Unlike eukaryotes, most bacteria have no junk DNA at all.  Copying the genome takes time.  When bacteria are dividing, those that are fastest will quickly take over.  Therefore, junk DNA is quickly discarded. Any gene that is not absolutely essential will be lost over time.  Bacteria are very thrifty in this way and this keeps complexity in check and keeps their genome trim.  Another constraint is size.  Bacteria respire through their cell membrane.  If a bacterium were to increase in size, it's surface area with respect to volume quickly plummets.  This makes it hard to generate the energy that it needs.  Therefore, it is not possible for bacteria to achieve the complexity of eukaryotes through the gradual Darwinian process of natural selection even over the billions of years they have existed.  Bacteria remain eternally bacteria.
As I discussed in an earlier post, eukaryotes escaped these bonds through symbiosis.  Our mitochondria freed us from a bacterial prison.  With mitochondrial to power us, cells could get bigger increase in complexity. 
So what is so special about mitochondria?  Are bacteria really eternally doomed?  Some bacteria have infolded cell walls to increase surface area, why couldn't this have gradually led to eukaryote-like complexity?  I will tackle these questions and more next time!

Origin of the Eukaryotic cell. A truly unlikely event.

According to Nick Lane in his books Life Ascending and Power, Sex, Suicide, the origin of the eukaryotic cell was truly an unlikely event.  If we could rewind the tape and try it again, chances are life would appear every time, but the appearance of eukaryotes was contingent on an unlikely chain of events.  Because of this, Lane doubts that life more complex than bacteria exists beyond earth. After all, after billions of years it only appeared once on earth.
We now know that the first eukaryote was formed by the merger of 2 prokaryotes.  The traditional idea of origins was that a primitive eukaryote engulfed the ancestor of our mitochondria since eukaryotes are known for phagocytosis, the abilty to engulf other cells.  However, this is probably not how it happened because the ability to engulf other cells requires energy.  It is now known that all eukaryotes either have mitochondria or have lost them at some point.  Lane believes that this links the origin of eukaryotes with the acquisition of mitochondria.  So, before the host cell acquired mitochondria, it wasn't going around engulfing other cells.  Lane suggests that perhaps the 2 prokaryotes started out their symbiotic relationship by living in close proximity and progressed over time to a one cell living inside the other.
Genetic studies suggest that host cell was a methanogen archea.  These cells are anaerobic meaning they survive on sulpher and stay away from oxygen.  This seems unlikely because if this were true, why did eukaryotes appear just as oxygen levels were rising?  As Lane points out, more oxygen means more sulphates because oxygen reacts with sulpher from volcanoes to produce sulphates.  But, as we all know, most eukaryotes thrive in the presence of oxygen.  Besides, what would use would a methenogen have for mitochondria which are useless without oxygen?  Lane believes that the most likely answer is that the ancestor of mitochondria had a diverse genetic toolkit.  Perhaps, it had the genes for utilizing hydrogen and oxygen.  Once it started supplying the hydrogen for the methanogen, it would no longer be dependent on deep sea vents and could venture off into oxygenated environments.  This primitive eukaryote would have had to adapt to the oxygenated environment before the mitochondria ancestor living inside it lost its oxygen utilizing genes through disuse.
This chain of events is just one way eukaryotes could have evolved.  The lesson here is that there were enough contingencies that the ascent beyond bacteria only happened once on earth in the billions of years that bacteria have populated the earth.  We are truly lucky to have made it through this bottleneck.  The biggest gulf in all of life is the divide between prokaryotes and eukaryotes.  We have more in common with a humble yeast cell than it does with a bacterium.

Bioinformatics and vertebrate hox cluster evolution

Last semester, I took Molecular Evolution and Bioinformatics.  It was such a blast!  For my final project, I compared hox cluster sequences of humans and other vertebrates with the non vertebrate chordate Amphioxus or Lancelet.  Most vertebrates have 4 hox clusters of 14 genes each.  Amphioxus has just 1 cluster of 14 genes.  It has been known for a while that in the vertebrate line the entire genome was duplicated twice which explains why most have 4 hox clusters.  For the most part these genes are well conserved across all chordates.  However, the posterior hox genes 10-14 are highly divergent.  Therefore, it is not known for sure how many hox genes the ancestral chordate had.  It could have had less than 14 and further duplications happened in each line after they diverged or the original chordate could have had 14.  I focused on the Amphihox 13 gene to determine it if it was closer to other amphihox genes or to the human hox 13 gene.  I conclude that it is most likely closer to the human hox 13 genes and therefore existed in the ancestral chordate.
My final paper is here and the presentation is here.
There is nothing earth shattering here. But, it could be interesting for anyone curious about what bioinformatics is all about.
Next semester, I will be working with my bioinformatics professor to automate bioinformatic analysis using scientific workflows.  So, there will definitely be much more on this topic in the future.

Culture evolves

Last semester at UVU I took a biology and culture topics course.  The intersection between culture and biology is a hot topic right now and I was completely enthralled.  At the end of the semester, we each had to do a presentation and write a paper on any topic that incorporates biology and culture.
I decided to write a paper on cultural evolution.  Specifically, does culture evolve and if so, does it progress in giant leaps or in small increments the way that biological evolution does.  This is an interesting question and I was actually surprised by the answer.  Logically, we might assume that cultural evolution progresses in giant leaps because unlike biological evolution, it is a guided process.  However, the evidence I present in the paper says that the opposite is the case.
I read a lot for this project and referenced a lot of sources.  The biggest and most important of these were the book Not By Genes Alone by Richerson and Boyd.  I highly recommend this book for anyone who wants to understand how culture evolves.  Some evolutionary thinkers such as Richard Dawkins have argued that culture evolves in a genelike way.  He calls them "memes".  Others such as Dan Sperber have argued that culumulative cultural evolution is not possible because culture is not faithfully transmitted like genes are.  Culture is transmitted analogously.  The way cultural traits are transmitted depend heavily on the idiosyncrasies of individuals.  However, Richerson and Boyd argue that culture definitely does evolve but memelike transmission is not necessary.  In fact, they say that a high mutation rate is actually necessary to prevent it from spiraling out of control!
You can download and read my complete paper here.  There was a powerpoint presentation that went with it and you can get that here.
More on this topic later.  Enjoy!