I recently read this at evolution news & views

Given the sheer number of these retroviruses in our genome (literally tens of thousands), and accounting for the evidence of integration preferences and site biases which I have documented above, what are the odds of finding a handful of ERV elements which have independently inserted themselves into the same locus?

I wouldn't bet on it. If I would have identified 2 TEs in humans and chimps exactly in the same genomic locus, I would predict that the most parsimonious event would be that the original insertion was in their primate ancestor. Of course, the scenario Jon M mentions is also possible, but it is a less likely scenario, since there are tens of thousands of possibilities for a TE to insert itself within large mammalian genomes.

Over at Pandasthumb there is a discussion about a very interesting study demonstrating the concepts of fitness landscapes and adaptive walks.

To summarize:

1) There is a target. In this study it was a substrate RNA immobilized on a magnetic bead.
2) The substrate RNA is a natural target for a class II ligase construct that "catalyzes the formation of a 2′-5′ phosphodiester bond between its 5′ triphosphate and the 3′ terminus".
3) Sequence pools of random RNA and variants of this ligase were generated.
4) These pools reacted with the immobilized RNA substrate.

And after a while, bingo, the pools of RNA mostly fit to bind to the substrate where "selected". The datasets from these reactions were used to generate a fitness landscape whereby the genotype (the gene sequence) was plotted against the phenotype (the function).

Read the rest of this entry »

After the discussion about toolkits and multi-cellularity a few more interesting discoveries were made. For example:
A) Oxygen is Key To 'Cut And Paste' Of Genes.
B) Sodium Channels Evolved Before Animals’ Nervous Systems, Research Shows. (h/t Mike Gene and Nullasalus)
C) Calcium is important for multicellularity and multi-cellular signaling.

These are also interesting facts to take into account:
A) Monosiga brevicollis has an extensive calcium signaling toolkit and emerged before the evolution of multi-cellular animals.
B) Choanoflagellates have five immunoglobulin domains, though they have no immune system; collagen, integrin and cadherin domains, though they have no skeleton or matrix binding cells together; and proteins called tyrosine kinases that are a key part of signaling between cells, even though Monosiga is not known to communicate, or at least does not form colonies.

Read the rest of this entry »

There are different approaches towards the concept of “teleology” and in many ways it is related to a particular view or concept of “matter” and “change”. The Scholastic approach towards matter and change are described here and here. The approach is Aristotelian by nature.  Darwin had good things to say about Aristotle. From Allan Gotthelf's article "Darwin on Aristotle": Darwin in a letter to William Ogle:

"Linnaeus and Cuvier have been my two gods, though in very different ways, but they were mere schoolboys to old Aristotle."

It is safe to say that Darwin did not model his concept of natural selection from an Aristotelian or Scholastic point of view as Gotthelf points out that Darwin was familiar with Aristotle's work but his respect for him only grew after he published The Origin. Mechanistic philosophy of matter and change was prevalent during Darwin's era. Paley's watchmaker analogy was the basis for the argument from design whereby reality was like a machine composed of parts with no intrinsic relationship between them. The designs in the system (or reality) were imposed from an outside agent.

Read the rest of this entry »

There are at least 24 different species concepts and none of them can be applied to all organisms that have ever lived (Hey, J. 2001). The Species Problem is a philosophical problem of biology that can be divided into two important questions that needs to be addressed. Before giving a proper definition of the term "species", the ontological status of the concept needs to be addressed and this is the first important question. Once the ontological status is cleared, the second question is how to adequately define the term "species" so that is can be used to properly catalogue all the different life-forms. In order to answer the first question, one needs to clarify whether the term "species" firstly refers to either individuals or classes (kinds) (1a) and secondly whether universals (classes being a kind of universal) are real or not (1b)? The Species Problem is of course relevant to biology in order to understand the process of speciation. Without a proper concept of the term species, speciation is unintelligible.

Read the rest of this entry »

The story goes that Socrates famously challenged the Sophists of Athens by constantly asking them "what is justice?", "what is good?", "what is right?" etc. as he was seeking the essence or nature of these concepts and not just some sophist's subjective opinion.

Plato developed his Theory of Forms. A Form from Plato's point of view is just an essence or a nature, the sort Socrates was looking for. For example, to know the nature of justice is to know just what distinguishes it from everything else that is not justice and this is just to know the Form of Justice.

Several questions then arise for example:
A) What kind of thing is a Form?
B) How does one know it?
C) Is it some physical object that is observable through our senses?
D) Is it just something subjective and just something we pick up from the use of language?
E) Where does it exist?

Read the rest of this entry »

Questions:

1) Do you agree with:
A) There is no necessary connection between cause and effect.
or
B) There is a necessary connection between cause and effect.

2) Do you agree with:
A) Regularity Theory for laws of nature
or
B) Necessitarian Theory for laws of nature

Read the rest of this entry »

Let's take the example of Fido, Brutus and Pluto, Sylvester, Felix and Garfield. Fido, Brutus and Pluto have the same identity, meaning they are all examples of Canis lupus familiaris. Sylvester, Felix and Garfield have the same identity, meaning they are all examples of Felis catus. Fido, Brutus and Pluto, Sylvester, Felix and Garfield are also distinct individuals (Figure 1).

Figure 1: Identity vs Individuality

Let's now apply these example to see how individuals and identities endure or perdure through change in 3-Dimensionalistic and 4-Dimensionalistic views of reality.

Read the rest of this entry »

What do you think is the relationship between time and change (change as in stuff changing position or from one thing to another etc.)?

A) Time exist as a result of or is a function of change. Time is an intellectual abstraction and a mathematical expression to quantify change. Without change there is no time sort of like without mass there is no gravity.
Or…
B) Time exists as some distinct (absolute or relative) entity and/or quantity and/or dimension that is different or distinct from the process of change. Time exists as an entity and/or quantity and/or dimension irrespective of whether there are things that are changing or not.

Read the rest of this entry »

Things change. I think we can all agree on this simple fact. Max Tegmark commented that "To me, an electron colliding with a positron and turning into a Z-boson feels about as intuitive as two colliding cars turning into a cruise ship".

There are at least three ways to describe changes. Local, substantial and property changes. To illustrate, let's use Max Tegmark's example:
Local change: An electron moves (changes position) from one place to another.
Property change: Change in the kinetic energy (kinetic energy being a property) of an electron.
Substantial change: An electron and a positron change to a Z-boson.

From a Scholastic view, annihilation and creation are different kinds of processes when compared change. For example, if an electron and positron turned into a Z-boson as a result of annihilation and creation, it would look something like this:

Figure 1: Annihilation and creation: The electron and positron get annihilated into nothing or nothingness and is the Z boson is created from nothing.

Read the rest of this entry »

People have differing world views, that much is a fact. Of course not all people’s world views are the same and logically speaking, not all people (with differing world views) can be right and hence why we have debates about them. One thing that is important in these debates is to take the effort to try and understand the world-view of another person or people you are debating with and also understand what arguments they have that supports their view. It is no use to try and criticize someone else’s view if you do not understand his/her position in the first place.

People have differing views with regards to the following concepts: Matter, change, creation ex nihilo, time, causation, natural laws, identity, substance, individuality,  etc. These concepts at the very core have philosophical and metaphysical implications. So for the next few posts I am going to try and flesh out the Scholastic approach to each of these and other concepts and contrast it with other approaches. At the end of the "interludes" I wish to show how the Scholastic approach can be relevant to scientific discussions especially related to biology. So to start off, let's look at the concept of "matter". There are at least three approaches; Atomistic, Aristotelian and Panpsychist.

Read the rest of this entry »