Genetics

Darwin’s Postulates & Firemouth Cichlids

Why cichlids?

Cichlid fish are one of the most biologically diverse groups of vertebrates on the planet. This diversity (as well as population size, reproduction rate, etc) allows scientists to study the cichlid evolution, and the role of natural selection, more closely than other populations. Many aspects of cichlid characteristics have undergone (and are currently undergoing) selective pressures. Cichlid evolution can be found at multiple levels, including behavioral changes, molecular adaptations, size and coloration variation.

Screen Shot 2014-07-24 at 10.42.50 AMThorichthys meeki is a species of cichlid commonly known as the “firemouth”, because of its bright red-orange coloration on the jaw. This specific coloration is unique to the firemouth, and is used in mating, competition and defense, and is therefore strongly affected by selective  pressures. In general, male firemouth cichlids have prominent  jawline coloration (10). The female Firemouth cichlids have specific molecular adaptations that that allow them to see the male coloration very clearly (6).

In the case of the firemouth cichlids, jawline coloration in males (and the subsequent female response) plays an important role in the evolution of the species due to the pressures of sexual selection. Sexual selection has been shown to be a mechanism of significant biological change for firemouth cichlids, even if the environment stays very stable (9), and research confirms that male coloration corresponds to sexual selection by the females (8). The females tend to mate with the more dominant males, so any characteristic that improves one’s chance of winning in a male-male competition scenario will be selected for. In any cichlid population, males who display the same color will compete more intensely. In firemouth cichlid populations, all of the males have a distinguishing red color, so male-male competition is very strong (4).

firemouthIt has been shown that smaller, less dominant males have physiological and behavioral changes during any social interaction with a more dominant cichlid. (3).  Many times, cichlids will engage in “pre-fight behaviors” (7) and  whichever male is smaller and duller will back down (5).    The coloration allows the more dominant males to emerge victorious from a fight with other males, without even having to engage in actual physical contact. The firemouth cichlids open their mouths and expose more of the red jawline. This behavior enlarges the head considerably when seen from the front and the side. In the event that there is no definitive pre-fight winner, they will engage in the more dangerous physical form of fighting. (1) In many cases, coloration is directly correlated to body size, which also plays a role in determining the winner of the conflict. (2) (more…)

Advertisements

Resource Recommendation: “Should America Prohibit Genetically Engineered Babies?”

Hi! A lot of things have been changing in my life lately, which caused this blog to take ‘back-burner’ status, unfortunately. However, I am giving myself a more strict posting schedule so that I can post stuff more consistently.
We’ll see whether or not my goals for this blog pan out!

Screen Shot 2014-04-15 at 9.49.55 PMAs some of you may know, I did an independent research project on genetic engineering and human children while attending Buff State. Before I started my research, I was under the impression that I would be arguing for a limited freedom perspective; where we should use genetic engineering for treatment and not for enhancement. However, as my research continued, I changed my mind to my ultimate conclusion: That we should have the moral (and likely legal) freedom to safely genetically engineer our children for both treatment and for enhancement. Not many people are comfortable with that conclusion due, at least in part, because genetic engineering (as a science) is relatively new. I can sympathize with that concern.
You can find that paper here: Genetic Engineering and Human Children

That being said, I strongly suggest anyone interested in the discussion of genetic engineering to check out this debate, hosted by Intelligence Squared Debates.

Should America Prohibit Genetically Engineered Babies?

The debaters are:
For the motion (we should prohibit genetically engineered babies):
Sheldon Krimsky & Robert Winston
Against the motion (we should not prohibit genetically engineered babies):
Nita A. Farahany & Lee M. Silver

For more information on the debaters and the event, NPR has a really good overview of everything, here: Should We Prohibit Genetically Engineered Babies? (debate audio included)

This discussion is really good, on both sides of the issue. If this is your first introduction to the topic, you may feel like you’re drinking from a firehose… but don’t worry. Its interesting enough for you to want to Google things afterwards (or likely during).

If this is the first time you’ve heard/seen Intelligence Squared Debates, you should definitely check out the other stuff they put out. It’s always incredibly interesting. You can find that here: Intelligence Squared Debates; Top Thinkers Debate Today’s Most Important Issues

Thanks for reading!
Feel free to leave a comment or question below 🙂

Cancer – What is it Anyway?

Scientia potentia est – knowledge is power

Many of you have likely encountered a kind of hype that is based almost entirely on the ignorance of the readers. People get a small glimpse into something they [rightfully] see as important, but because they don’t really understand it… they end up drawing erroneous conclusions.

Lets face it: many people don’t really understand cancer.
Its a difficult disease to understand, and people will often assume that there is some easy cure ‘out there’ and it is being concealed/ignored because cancer research facilities are just in it for the money (or… you know… something like that).

The first step in correcting this misconception is to understand what cancer is. With a proper understanding of the complexities of cancer, we can (hopefully) communicate this with people who do not understand it.

So while this post may not be as argumentative or provocative as some of my other posts, it is just as (if not more) important.
Scientia potentia est.

Without further ado:
Cancer – What is it Anyway?

cancer_cell_0604 Cancer is the name given to a large group of diseases  that behave in a variety of different ways, depending  on the type of cell from which they originate. Broadly  speaking, cancer is associated with at least two  primary symptoms: uncontrolled cell division and  metastasis. In normal cells, the cell cycle is a tightly  regulated system that is highly controlled and  managed by proteins, enzymes and the corresponding  genes on the DNA molecule. In some cells, however, the regulations of normal cell processes are interrupted/altered by mutations. These mutations cause many genes to be expressed inappropriately, and this can lead to cancer.

(more…)

Genetic Engineering and Human Children

regulate-designer-babies_1Most of us would do anything to help our children have the best future possible. We would make sure they had the best prenatal environment, the best diet and be sent to the best schools, all so that they could have the best possible future opportunities. But what would we do if we could, before they were born, alter our child’s genes in order to guarantee that advantage? The choice of genetically engineering our children is rapidly becoming a scientific reality, and we are faced with the question: If we are able to safely engineer a child at the genetic level… should we?

Genetic engineering is a topic that is greeted with a combination of curiosity, skepticism and apprehension. Those in favor of genetic engineering have been accused of “playing God”, whereas those opposed have been characterized as being against scientific progress. Many people view genetic engineering as something confined to the domain of science fiction; something so far in the future that it needn’t be worried about. However, with the advance of modern technology, this attitude towards genetic engineering is not only misguided, but can be dangerous.

Nearly every advance in technology comes with unanswered questions, and genetic engineering is no different. What should we do? What will happen if we make certain decisions? How will our decisions affect society? If we have the ability to do it safely, is it ethically permissible to genetically engineer our children? Is there an ethical difference between genetic enhancement and genetic  therapy? As people living in the time where genetic engineering is a real possibility, it is vital that we address the bioethical issues surrounding this controversial topic. If we procrastinate in this area and do not address these issues before they  come up, we will inevitably make poor decisions that could have been avoided. Like  many advancements in science and technology, genetics provides us with an  opportunity to be good stewards with what we have. But it also offers us a unique  opportunity as well; “… we can begin to determine not simply who will live and who will die, but what all those who live in the future will be like” (Harris & Burley, 2004)

p016q9gp This article is designed as a form of philosophical preventative maintenance,  with very real ramifications for the near future. Because it is meant to address  issues of genetic engineering specifically, other issues will be avoided. I will  assume that genetic engineering will not destroy human embryos and will not  result in any unintended changes. These issues need to be addressed by  scientists, doctors and ethicists today, but will likely be circumvented with the  advance of technology. The purpose of this paper is to ask, “What philosophical  issues arise from genetic engineering itself?”

Many moral philosophers and ethicists, when approaching complex ethical issues, have attempted to lay out a principle of moral reasoning that is designed to answer the question, “what ought I to do?” It seems reasonable, therefore, to follow a basic principle of moral reasoning, and philosopher Kurt Baier explores a fairly simple one in his book, “The Moral Point of View”. According to Baier, “The best course of action is… the course of action which is supported by the best reasons. And the best reasons may require us to abandon the aim we actually have set our heart on.” Baier’s two-step approach involves looking at the relevant facts surrounding an issue and determining the relative weight of those considerations “to decide which course of action has the full weight of reason behind it”. (Baier, 1969) Following this approach, it is our job to critically examine the arguments for and against genetic engineering and to support the most reasonable conclusion, given the strongest available arguments on both sides. (more…)

Newly Discovered Functions of “Pseudogenes”

Abstract

Researchers have noted that there are portions of the DNA that look similar to functional genes, but contain lesions or premature stop codons. These genes have been assumed to be largely non-functional, but recent research suggests that many of these ‘pseudogenes’ are actually functional.  This paper is an overview of some of the research done in the area of  pseudogene functionality. I address several recent advances in the  area of genetic research regarding pseudogene functionality  chronologically, starting from one of the first discoveries of a  functional pseudogene and ending with a paper from this year (2013). Broadly speaking, it would seem that the assumption of non-functionality has been overturned regarding many pseudogenes, and the evidence suggests that many more pseudogenes may have a function that has yet to be discovered.

Introduction
pseudogene_important_role_wide Pseudogenes have been typically understood as portions of DNA  that have lost their function and remain in the DNA as a relic that  signifies past functionality. The prefix ‘pseudo-‘ indicates that  something is fake or false, and a pseudogene is a portion of DNA  that looks like a functioning gene, but is not actually functional. Pseudogenes have been placed in the ‘junk DNA’ category, ‘dead’, non-functional by-products of evolution. If a pseudogene is transcribed at all, it is often considered to be largely a neutral process that hasn’t been weeded out by selection. However, recent evidence has shown that many pseudogenes have very important functions in the genome of nearly every organism, humans included. There are very good reasons to revise the definition of ‘pseudogene’ to include a wide variety of biological functions, from gene expression and cellular function to gene regulation and tumor suppression. The newly discovered functions are making the term ‘pseudogene’ notoriously ambiguous. This review will analyze a small handful of functions discovered for pseudogenes that were previously assumed to be non-functional byproducts of genome evolution. It is not intended to be an exhaustive treatment of newly discovered pseudogene functionality. Functions are being ascribed to pseudogenes on a fairly regular basis in contemporary genetics literature, and some of the literature is reviewed in chronological order.
(more…)

Homo sapiens, Neanderthals and Denisovans… did they interbreed?

Recent discoveries in DNA have shed light on the relationship of Homo sapiens and extinct hominids, Homo neanderthalensis and Denisova hominins. There is evidence to suggest that all three lived around the same time, and possibly in the same area (Krause et al., 2010)(Meyer et al., 2012). If these three groups lived close together, it should be possible to detect whether or not theyinterbred. If H. sapiens interbred with H. neanderthalensis and D. hominins, we should be able to find genetic evidence of this interbreeding in modern H. sapiens genomes. Using modern genetic examination (Gibbons, 2010), scientists have determined that H. sapiens did interbreed with both H. neanderthalensis (Green et al, 2010)(Hawks, 2013)(Meyer et al, 2012) and with D. hominins (Hawks, 2013)(Meyer et al, 2012).

article-1058538-02B984B100000578-348_468x342Homo neanderthalensis fossils were first discovered in 1856 in Germany, and ever since, scientists have been exploring the relationship of Neanderthals to modern humans. (Gibbons, 2012) The first “draft sequence of the Neanderthal genome” was published in 2010 (Green, et al), and that has given us insight into the relationship of Neanderthal DNA to the DNA of modern humans. Using data obtained by the Human Genome Project (Intl Human Genome Sequencing Consortium, 2001), scientists can compare human and Neanderthal DNA in order to discover the genetic relationship between the two.  The evidence suggests that Neanderthals lived in both Europe and Asia before going extinct around 30,000 years ago (Green et al, 2010). However, many of the Neanderthals interbred with H. sapiens before going extinct. According to Green and colleagues (2010) andHawks (2013), modern humans living outside of Africa represent between 1% and 4% of ancestry from Neanderthal populations. It is possible, with modern genomic technology, for the average person to send a sample of her own DNA to a lab (ex: ‘23andMe’) and get results showing her ancestry. If she has European ancestry, it is possible that she will also have some small percentage of Neanderthal ancestry (Gibbons, 2012). These sorts of results would only be possible had the Neanderthals interbred with direct ancestors of modern humans. Not all of the evidence suggests that Neanderthals interbred with the ancestors of modern humans, however. A study showed that there were no contributions from Neanderthal mtDNA to modern human mtDNA from a specimen recovered from Mezmaiskaya Cave in the northern Caucasus. (Ovchinnikov, 2000) This is not necessarily contradictory data from the other studies; it shows that not all Neanderthal populations interbred with modern human populations.
(more…)