I’ve been following the current round of US primaries with some interest. Not ever having visited the US, I have no business criticizing the system or the candidates but I must admit to being fascinated by the progress of Donald Trump and the seemingly growing possibility that he may become the Republican presidential candidate. Presumably, there is also the possibility that he could become the next President of the United States. Continue reading
“Intentionality” is a philosophical term for “aboutness”. A movie review is about a movie, and the sentence “Trump is a narcissist” is about Trump. Your thoughts concerning today’s breakfast are about today’s breakfast. Each of these is about something else, so each exhibits intentionality.
How do these things acquire their aboutness? “Trump is a narcissist” isn’t inherently about the man who bears the name “Donald Trump”. Had Trump’s family retained their Germanic surname, Drumpf, then “Trump is a narcissist” would no longer be about the man we call “the Donald”. The intentionality of the sentence is derivative; that is, it derives from the pre-existing convention of referring to a particular man as “Donald Trump”.
TSZ has made much ado about P(T|H), a conditional probability based on a materialistic hypothesis. They don’t seem to realize that H pertains to their position and that H cannot be had means their position is untestable. The only reason the conditional probability exists in the first place is due to the fact that the claims of evolutionists cannot be directly tested in a lab. If their claims could be directly tested then there wouldn’t be any need for a conditional probability.
If P(T|H) cannot be calculated it is due to the failure of evolutionists to provide H and their failure to find experimental evidence to support their claims.
I know what the complaints are going to be- “It is Dembski’s metric”- but yet it is in relation to your position and it wouldn’t exist if you actually had something that could be scientifically tested.
DNA is not just a static read-only memory (ROM) for coding proteins, but hosts dynamic random access memory (RAM) in the form of methylations and histone modifications for regulation of gene expression, cellular differentiation, learning and cognition, and who knows what else. The picture below depicts how rapidly the RAM aspect of DNA is changed during embryogenesis.
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There are a few reasons this OP could be a flop.
1. It links to an article by Ed Feser.
2. It raises issues of teleology and teleonomy (again).
In any event, for those interested in the subject I think Feser’s article is worth a read.
It is here proposed that the evolution of life was destined to produce self consciousness out of physical matter just as surely as self-consciousness is destined to be produced by the build up of matter from the human zygote.
Our external vantage point allows us to see the process whereby an individual human matures from the point of conception We are in a position to witness all the stages in the life of individual humans. Activities such as birth, death, growth and decay go on all around us. Conversely on the grand scale of things, taking life as a whole, we are in the middle of evolving life and so we don’t have an overall, clear picture of the process.
In this video Sean B. Carroll states that:
…living things are occupying a planet whose surface is always changing. Hurricanes, earthquakes, volcanoes, tectonic movement, ice ages, climate changes whether local or global, all of these keep changing the environments that species are in, they are running to keep up and most of the time they fail. So we have to think about earth’s history to understand life’s history. We have to understand what’s going on at any particular place to appreciate what’s going on with any particular species.
The same could be said for the cells in your body. Their environment is always changing and most of them do not survive as you change from embryo to adult. From an individual cell’s point of view there may not seem to be any direction.Some live some die, some change slowly, others change dramatically. But from the higher perspective of the whole body there certainly is direction.
Can money buy happiness? These people, waiting for hours to buy lottery tickets, seem to think so, or at least are willing to test the hypothesis (turn off your sound — the commentary is annoying):
What does science say? The short answer is that money can buy happiness, at least up to a point. The long answer is quite complicated.
Recent discussions of genetic algorithms here and Dave Thomas’ evisceration of Winston Ewert’s review of several genetic algorithms at The Panda’s Thumb prompted me to dust off my notes and ev implementation.
In the spring of 1984, Thomas Schneider submitted his Ph.D thesis demonstrating that the information content of DNA binding sites closely approximates the information required to identify the sites in the genome. In the week between submitting his thesis and defending it, he wrote a software simulation to confirm that the behavior he observed in biological organisms could arise from a subset of known evolutionary mechanisms. Specifically, starting from a completely random population, he used only point mutations and simple fitness-based selection to create the next generation.
The function of ev is to explain and model an observation about natural systems.
— Thomas D. Schneider
There’s a deep and fascinating question about whether we need “foundations” in our philosophical system, and if so, why and what kind.
First question: is the foundationalism primarily epistemological (foundations of knowledge) or ontological (foundations of being)?*
Second question: insofar as foundationalism implies a hierarchy, is the grounding or fundamental principle at the top of the hierarchy or at the bottom?
These two questions give us four positions:
top-down epistemological foundationalism: rationalism
bottom-up epistemological foundationalism: empiricism
top-down ontological foundationalism: theism/idealism
bottom-up ontological foundationalism: materialism
The ontological foundationalism can be reductive or non-reductive. Hence:
reductive top-down ontological foundationalism: idealism
non-reductive top-down ontological foundationalism: emanationism
reductive bottom-up ontological foundationalism: physicalism
non-reductive bottom-up ontological foundationalism: emergentism
Likewise, anti-foundationalism can also be epistemological or ontological:
epistemological anti-foundationalism: pragmatism (or: the good parts of Hegel/Peirce/Sellars)*
ontological anti-foundationalism: process ontology (or: the good parts of Spinoza/Whitehead/Deleuze)*
The main reason why I have resisted efforts to interpret me as an empiricist or materialist is that both empiricism and materialism are forms of foundationalism. Since I am an anti-foundationalist (both in epistemology and in ontology) I am as opposed to empiricism as I am to rationalism, and as opposed to materialism as I am to theism. My views might look like those of an empiricist/physicalist, but only if one insists on interpreting those views through the lens of the foundationalism that I reject.
As time permits I’ll explore the arguments for epistemological anti-foundationalism and ontological anti-foundationalism. For now I just wanted to get the conversation started.
*I’m leaving aside ethical and political versions of foundationalism and anti-foundationalism, though I think that’s where the philosophical action is really at.
** I’m only citing philosophers in the Western canon here, but Nagarjuna in the Madhyamika tradition of Tibetan Buddhism developed a consistently anti-foundationalist epistemology and ontology one and a half millennia before it was even conceived of in the West. Within the West, probably Nietzsche and Dewey would be the first consistently anti-foundationalist philosophers.
The emergence of life for the first time on this planet constitutes the classic question of what came first; the chicken or the egg?! Did a self-replicating DNA system occur before transcription or translation evolved (the DNA World) or did a self-replicating RNA system first emerge (the RNA world) or did self-replicating protein system first emerge (the Protein World)…or … let’s just leave it there for now. Continue reading
This is just an effort to help keep Joe’s thread focused and to help keep it from being derailed. People can use it or not. I hope they will.
CharlieM: Can someone explain to me, why is all of this not just a model of directed evolution? Surely it is set up to be directed towards a target?
Richard Dawkins’s computer simulation algorithm explores how long it takes a 28-letter-long phrase to evolve to become the phrase “Methinks it is like a weasel”. The Weasel program has a single example of the phrase which produces a number of offspring, with each letter subject to mutation, where there are 27 possible letters, the 26 letters A-Z and a space. The offspring that is closest to that target replaces the single parent. The purpose of the program is to show that creationist orators who argue that evolutionary biology explains adaptations by “chance” are misleading their audiences. Pure random mutation without any selection would lead to a random sequence of 28-letter phrases. There are 
possible 28-letter phrases, so it should take about 
different phrases before we found the target. That is without arranging that the phrase that replaces the parent is the one closest to the target. Once that highly nonrandom condition is imposed, the number of generations to success drops dramatically, from to mere thousands.
Although Dawkins’s Weasel algorithm is a dramatic success at making clear the difference between pure “chance” and selection, it differs from standard evolutionary models. It has only one haploid adult in each generation, and since the offspring that is most fit is always chosen, the strength of selection is in effect infinite. How does this compare to the standard Wright-Fisher model of theoretical population genetics? Continue reading
I would be grateful if somebody could help me out here as Bioinformatics is not my strong card.
Regarding the recent Nature publication
New deep-sea species of Xenoturbella and the position of Xenacoelomorpha
I query the authors’ explanation; to wit…
The sister group relationship between Nephrozoa and
Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.
My problem arises with their placement of Ctenophora on their own phylogenetic tree as the “more primitive out-group” (for lack of better words on the spur of a rushed moment). Myself, I always considered Ctenophora as bilateral – in this case more primitively bilateral which IMHO should root the bilateran tree… which of course begs more than one question upon rereading their analysis.
Forget Ctenophores – what about Cnidarians!? Some taxonomists argue that Cnidarians are descendents of ancient bilateral coelomates and not the other way around. Biologists have known since the 1920s that Cnideria had a directive axis which gave them right and left-hand sides. Volker Schmidt goes on to argue that non-radially organized hydrozoan larvae have an anterior concentration of sensory and ganglionic nerve elements, suggesting that a fundamental genetic toolkit for the establishment of bilateral and polarized anatomies was already present before the Cnidaria-Bilateria divergence. Volker Schmidt goes so far as to suggest that diploblastic status of adult Cniderians is derived and that true mesoderm can be even be detected during Cniderian embryogenesis. OK – I concede that last argument is particularly contentious… but you get my drift.
I am partial to the notion the UrBilateran that subsequently gave rise to “Protostomes” & Deuterostomes and was itself coelomate with possessed a dorsal nerve chord. Any subsequent acoelomy and pseudocoelomy was derived… ditto ventral nerve chords. But hey… now I am being really contentious!
Michael Behe is best known for coining the phrase Irreducible Complexity, but I think his likening of biological systems to Rube Goldberg machines is a better way to frame the problem of evolving the black boxes and the other extravagances of the biological world.
Continue reading
In his endless pursuit of that wascally Weasel, Mung made the following silly claim:
GAs are often used to demonstrate “the power of cumulative selection.” Given small population sizes drift ought to dominate yet in GAs drift does not dominate.
That is clearly false, but for the benefit of Mung (and his cousin Elmer) I have modified my Weasel program to incorporate both drift and selection. They can now see for themselves that small population sizes are insufficient to guarantee that drift dominates selection.
The code is here. Compile it under Linux using “gcc -std=gnu99 -lm weasel.c -o weasel”.
I am reading a book in which the authors set forth the evils of belief in “The Great Chain of Being.”
The Great Chain of Being is, in fact, firmly ingrained in our culture and spirits. It leads to certain grave errors that are commonly acknowledged but difficult for teachers to correct.
The first of these is Anthropocentrism, “the view that man is the measure of all things.”
My favorite subject-specific journal is Molecular Biology and Evolution (MBE). This journal publishes on topics primarily related to molecular evolution and evolutionary genomics, which are among my favorite subjects in biology. I’m happy to report that the latest issue of MBE is out today, and there are lots of great articles that I think will be of interest to folks here, many of which are open-access.
I sadly don’t have time to write up any of these articles, but I thought it might be useful to “sample” a few in case any any of you would like to read and discuss them. Here are a handful that seem particularly interesting:
Cross-posted from UD: The Alternatives to Methodological Naturalism conference is doing a design contest with a cash prize.
Among Christianity’s many odd doctrines is the notion of original sin. The details vary from denomination to denomination, but a common view is that all humans are born into a state of sin because Adam succumbed to temptation in the Garden of Eden, and that this state of sin makes us worthy of God’s eternal condemnation. Only Christ’s sacrifice can redeem us.
Throughout the history of evolutionary biology, as well as many other sciences, there has been a conflict between two styles of thinking. One is conventionally called functionalism, although in evolutionary biology the term “adaptationism” is more frequently used today because a trait’s “functional fit for it’s office” is produced through adaptation by natural selection (i.e., function is explained by adaptation through natural selection). The functionalist stance is one that explains organismal traits through their functional and adaptive values.
The alternative style of thinking does not have a generic name in biology, although in other areas of study it is called “structuralist.”
Michael Denton in Evolution: Still A Theory In Crisis or Gunter P. Wagner in The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism?