Cavalcade of Mammals

I understand PZ’s point, that the information in DNA is expressed through and requires the cell (cytoplasm, nucleoplasm, etc). But the cell is self-assembling–put a human nucleus in a mouse cell, let it divide a dozen times, (maybe a hundred times), and now you have completely human cell. Cloned animals have epigenetic-derived defects, but I expect their Nth generation offspring will be normal.

Let me push the argument further taking a bacterial cell as the model. In principle, you could express proteins in vitro and combine them with lipids, small molecules, and DNA and reconstitute a cell. It wouldn’t be quite right, but get it close enough that it can divide, let it do so a bunch of times and then the cell will be completely normal.

But which proteins would you express and how would you figure out how to combine them? In principle, you could predict from the DNA sequence the set expressed in a particular environment, relative expression levels, and where they go–membrane, cytoplasm, etc.

True enough, DNA without its cellular environment is not a cell, and in biological systems the DNA is always associated with its cell, but the epigenetic information is mainly derived from the DNA and secondary to it. For the biologist this distinction is meaningless–practically we can’t yet predict epigenetic context from DNA or recreate it from scratch. Biologists describe the epigenetic state, observe it and assay for it.

PS Meyers has blog post criticizing a creationist describing organisms as computer programs, and then arguing from incredulity against naturalistic explanations for human development. That’s well and good, the creationist is an idiot, but then Meyers takes it a step further and expresses a dislike of software-type descriptions of development:

The genome is not code, efficient or otherwise. Sure, you can tally up the bits needed to store the sequence in a database, but that is not the same as saying you’ve got the complete information for an organism, or that you have captured the “code” that can be executed to build it.

I’m happy to think of the genome as a program. At the high estimate, 100 million bits (25000 genes * 1000 bps per gene * 1000 bps of regulatory seq per gene * 2 bits per bp) or 12Mb to describe the human genome.

So a fairly small amount of code is enough to generate a person. The small number is clearly enough–it is what humans develop with. The program isn’t written in a bloated computer language. It’s more like hand-tuned (or genetic algorithm-tuned, ha) assembly code, full of GOTO statements and with enough cross connected subroutines to make the block diagram look knotted as a ball of thread.

The size doesn’t seem small in relation to the code. Look at the Mandelbrot Set, 7 bytes to write it down and an incredibly complex result. So clearly a small program can produce a complex result.

PZ considers epigenesis important and a reason to reject the computer program hypothesis as insufficient. Epigenesis is clearly important but I don’t see it as a reason to reject the computer program analogy. The epigenetic information is an expression of the genomic program.

Also, calling the genome a library of components seems too static to me. “Library of subroutines” or “library of services” captures the sense of what is going on better, with different subsets of routines active at any time.

It is interesting to compare computer programs with living organisms, but as this creationist shows it is easy to be mislead (or to mislead) by the analogy. I think any complete description of cellular activity and development will use the concepts used to describe computer programs.

Humans point. Pointing is instinctive in humans. Babies instinctively point to things and pay attention to pointing. They know it is communication. I saw this neat stuff on a Nova episode on ape learning. It mentioned that chimps don’t understand pointing. It’s strange to watch. They don’t do it instinctively and don’t understand it.

Also, apparently we have selected dogs to understand pointing.

Always fascinating, on the sexual practices of Papua New Guinea:

The Dobo, who live on a small island off the coast of the main island, live in constant fear of sorcery from their wives. Because they believe that they are particularly vulnerable during intercourse, Dobo men have to continually weigh their need for sexual gratification against the possibility of sorcery when they try to satisfy their sexual need (Davenport 1997, 126).

Much of it makes for disturbing reading. Papua New Guinea is a terrible place.

It’s recently come out that National Review Online (the US’s top Republican political magazine) published fake reporting of massive (and apparently imaginary) Hezbollah invasions into the Christian section of Beirut written by reporter W. Thomas Smith Jr.

He also wrote The Complete Idiot’s Guide to Understanding Intelligent Design. Who could have guessed he wasn’t a reliable source of information?

It gets even funnier. The publisher-supplied description on Amazon says the book was “Written by an expert in the field”. Ha! Neither one of them is a biologist. And better yet, Smith is described there as having written “thousands of articles for a variety of publications”. Which comes to more than two a week, for twenty years straight. Sounds like exaggeration, though this time written by the publisher.

It was announced today that the full genomes of James D. Watson (and Craig Venter, though for much more than $1,000,000) have been sequenced. The NYT article had this bioethics blurb:

Dr. Watson and Dr. Venter are both taking a considerable personal risk in making their genomes publicly available. As is probably true for everyone, their genomes are likely to contain mutations that could lead to disease, revealing possibly unfavorable information about themselves and their relatives.

For Venter this is clearly untrue. He’s rich and can self insure with no problem. Likely Watson has enough dough this isn’t a risk either. For their poorer relatives, yes there is risk. I don’t think the writer of the NYT article, Nicholas Wade, gave this any thought–genetic knowledge insurance/employment risk is a standard story line, and the writer plugged it into this article.

A company has developed a new reading technology called Live Ink (paper here). The idea is to improve the way text is displayed to improve reading comprehension. The way the brain perceives a page of text is as small region at a time. Words from several lines get picked up at the same time. This confuses the parts of the brain that comprehend words and sentences. Live Ink proposed to spread text out to avoid this mental confusion to improve reading comprehension.

There’s a kernal of a good idea there–electronic text allows reformatting to increase comprehension. But their solution sucks. It takes up too much space and it only partially helps with the problem of line confusion. The syntactic breakup may be helpful. Here’s an image of it:

Computer formatting is a good idea. Here is my idea of how to do it. Fuzz out the lines before and after the current line. This could be done one of two ways. If eye movement tracking is available, follow the eye and only make the line being looked at visible with the others fuzzed out. Without eye tracking make this a timed system (like traditional light bar reading trainers). Start it on a section of text and make one line at a time is visible moving through the text. Controls would be needed to pause and go back a few lines, and flip it off.

By fuzz out the rest of the page I mean alter it so the brain doesn’t think it is text and try to decode it. Whether making it out of focus is enough or if another kind of noise needs to be added would need to be determined by trials. It would be important to leave enough information that the presence of text blocks and formatting is visible. These provide visual landmarks needed for good reading.

Technically, this could be easy–a web browser extension or perhaps as simple as some Javascript added to a page with overlay images fuzzing the text and moving as needed.

Well done site that explains stem cells to the public:
http://www.tellmeaboutstemcells.org/

Old doggerel, but new to me:

“Let’s consider the concept of niche-
If I knew what it meant I’d be rich.
Its dimensions are n
But a knowledge of Zen
Is required to fathom the bitch.”