Junk for Brains

petrushka:

It’s slightly surprising how many people are willing to judge the efficacy of GA’s without being able to write one, even at the specification or pseudocode level.

That's a straw-man. People are not judging the efficacy of GA's. And I wonder how many of you over there at TSZ who are pontificating on these subjects can meet your requirements.

This really ought to be a prerequisite to discussing evolution.

lol. What does knowing how to code a GA have to do with evolution? Mung

And today's Junk for Brains winner is: onlooker@TSZ:

Others here have noted that you are confusing the model and what is being modeled. Labeling all GA fitness functions as “active selection” misses the point of what the fitness function is modeling....All the fitness function is modeling is that environment.

So let's just ignore what the fitness function actually does and how it is able to do it and just pretend that it's just a model of an environment. And if you refuse to ignore the facts and pretend with us, well, you're just confusing the model with what's being modeled. The environment has no goal, purpose or function in mind. It's not trying to use organisms to solve some problem. It's purpose is not to direct organisms towards possible solutions to a pre-specified problem. Unless you believe it's all part of some grand design, that is. Mung

p.s. Surely no one else has ever tried to model biological mechanisms with math. Mung

Toronto:

Biology is real and chemistry and physics determine what happens from one generation to the next. Dembski errs when he tries to model biological mechanisms with math.

It's ok to model physics with math. It's ok to model chemistry with math. Biology is just physics and chemistry. Dembski errs when he tries to model biological mechanisms with math. Mung

Mike Elzinga:

Don’t ever make the mistake that we are using YOUR “rules” in our programs. YOUR rules don’t work because they were concocted for other reasons. They were not derived from the study of the physical universe.

Not that Mike has never himself used a rule that was not derived from the study of the physical universe. That just wouldn't do. Mung

Mike Elzinga:

So stop the war and go out and study the world around you. And, please, do benefit from what we already have learned.

Mike's learned everything is there to learn, and that is why he spends his time posting on an internet blog rather than being out there practicing what he preaches. Mung

petrushka:

Only in laboratory condtions do we encounter such narrow kinds of selection.

And in GA's. Mung

keiths@TSZ:

You cannot be serious. In less than 48 hours, you’ve taken three mutually inconsistent positions. First you told us that GAs are invalid as models of NS because they’re designed: Then you retracted that statement, asserting instead that it’s okay that GAs are designed, as long as they don’t have fitness functions: "gpuccio: Any fitness function in any GA is intelligent selection, and in no way it models NS."

A GA without a fitness function isn't much of a GA. So that's hardly mutually inconsistent. And a statement that any fitness function in any GA in no way models NS is not inconsistent with a statement that GAs are invalid as models of NS. So, it was otherwise a close contest, but you win the "junk for brains" award for today. grats Mung

Toronto:

Your side is still at the point of learning what “simulation” means, never mind a practical application.

And just what is it that Lizzie's program simulates? Natural Selection? Really? Mung

Toronto:

The “mechanism” of evolution has no target.

Then stop claiming GA's model of evolution and that GA's demonstrate what evolution can do. Mung

Toronto:

We could also use the “Lizzie” algorithm to perform “Methinks it is like a weasel”, without changing the algorithm but simply changing the “environment”.

That I have to see. Mung

Zachriel:

Presumably, Mendel's Accountant is considering absolute fitness, meaning populations can precipitously degrade if the fecundity drops below a certain level. If they were serious, they would investigate under which circumstances they would not see meltdown, and explore this boundary in more detail. But their purpose is apologetics dressed up as science. I certainly wouldn't consider any such simulation to be anything more than qualitatative unless carefully matched to a biological situation. It doesn't even account for sexual selection; and without empirical verification, it is subject to simple mistakes such as the calculation of "working fitness" noted above. They see what they want to see.

We'll await the results of the empirical verification of Lizzie's simulation. Mung

Junk For Brains I'll have to try to remember to post responses to posts at TSZ in this thread. Junk For Brains is so apropos. Mung

http://find.lifetechnologies.com/events/aacr2012b/gdn Mung

PaV: Hi, old friend! Always spot on, as usual. The procedures, the procedures: we are starting to understand a little bit of the procedures, at last. That will really mean a "new bad era" for darwinists. gpuccio

It's always nice to see some science news posted here. JoeCoder

I've fixed the link, BA77. Thanks. Your link to the NIH is about the same paper. What's interesting here, IMO, is that a particular organ (pineal) in an extremely complex other organ (the brain) shows itself to have a very important function. We sometimes forget that huge variety of cell-types that exist within the mammalian body-type. And what might be of very little utility to a muscle cell might be of very great utility in the retina; and, yet, all of this information must be handed down. I think this paper unveils for us a better way of looking at, and understanding, the structure of the genome. PaV

a few more notes along that line:

Long Noncoding RNAs with Enhancer-like Function in Human Cells - 2010 Excerpt: While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation. http://www.sciencedirect.com/science/article/pii/S0092867410010111 Researchers discover molecular determinant of cell identity - March 2011 More 'Junk DNA' bites the dust; For years, many biochemists were skeptical that lincRNA played any important role in a cell and considered the molecules just mere "noise," perhaps vestigial protein-coding genes that had mutated to become nonfunctional., lincRNAs play a critical regulatory role: determining what proteins a cell produces and, thereby, what identity it assumes" http://www.physorg.com/news/2011-03-molecular-cell-identity.html Long Non-coding RNA Punches Another Hole in "Junk Genome" Myth - December 2011 Excerpt: cellular processes are not only highly complex, but highly regulated. As the authors of this study point out, "these results revealed a novel layer of regulation of erythroid cell differentiation and apoptosis by a lincRNA." When we consider that many aspects of the cell are highly regulated, we find that the cell operates like a factory with an intricately woven network of processes rather than a hodge-podge of functioning and non-functioning pieces of the kind you might expect to result from a randomly driven evolutionary process. With every discovery of additional layers of complexity and regulation in the cell, we see the hallmarks of engineered or designed processes. http://www.evolutionnews.org/2011/12/long_non-coding054291.html Reference Notes For Jonathan Wells' Book - The Myth Of Junk DNA - Hundreds of Studies Outlining Function for What were Supposedly 'Junk' DNA regions http://docs.google.com/viewer?a=v&q=cache:zGp3gRRDmA0J:www.discovery.org/scripts/viewDB/filesDB-download.php%3Fcommand%3Ddownload%26id%3D7651+Sequence-dependent+and+sequence-independent+functions+of+%E2%80%9Cjunk%E2%80%9D+DNA:+do+we+need+an+expanded+concept+of+biological+information%3F+Jonathan+Wells&hl=en&gl=us&pid=bl&srcid=ADGEESiCq0TQUSKYlr0KNNIDgaGKMM7b3z0iEGiKe_faSd0646SzaYSoCCcNavm523X5TgaGbdQPtDFmN6Yw8IexI44RokfsMKs6q-EEeM_vyYw-zaMB-h_7wKu8JjGREn_JF-CPlkSq&sig=AHIEtbRfG8rv_5eur2oifBsWxHdM_e731g

bornagain77

PAV, the link did not work. Perhaps this paper?

Dark matter DNA active in brain during day — night cycle - Sept. 21, 2012 Excerpt: "These lncRNAs come from areas of the genome that we thought were quiet,",,,"But current research in the field makes it unequivocally clear that the information-carrying capacity of the genome is a lot greater than we realized previously." http://www.nih.gov/news/health/sep2012/nichd-21.htm

bornagain77