Re: Issues

On Fri, 8 Jul 2005 17:06:05 -0400 (EDT),
Perplexed in Peoria <jimmenegay@xxxxxxxxxxxxx> wrote:

[snip]

> The 100 issues on the "second tier" are listed here:
> http://www.sciencemag.org/cgi/content/full/309/5731/78b
>
> I am particularly interested in these two:
>
> What enables cellular components to copy themselves independent
> of DNA? Centrosomes, which help pull apart paired chromosomes,
> and other organelles replicate on their own time, without DNA's
> guidance. This independence still defies explanation.
>
> Who was LUCA (the last universal common ancestor)?
> Ideas about the origin of the 1.5-billion-year-old "mother" of all
> complex organisms abound. The continued discovery of primitive
> microbes, along with comparative genomics, should help resolve
> life's deep past.
>
> Does anyone know know where that number 1.5-billion came from?
> I would have guessed at least a billion years earlier. They can't
> be restricting the U of the term LUCA to the eukaryotes, can they?

Some of the questions are very strange. Here's some more ...

"What is the origin of homochirality in nature?
Most biomolecules can be synthesized in mirror-image shapes.
Yet in organisms, amino acids are always left-handed, and sugars
are always right-handed. The origins of this preference remain
a mystery."

We have some pretty good ideas about this. I'd hardly call it a
major mystery. Mostly it's a frozen accident like the origin of the
genetic code. (Which, incidently, didn't make the list.)

"Can we predict how proteins will fold?
Out of a near infinitude of possible ways to fold, a protein
picks one in just tens of microseconds. The same task takes 30
years of computer time."

This is a major area of research. I think there's general agreement
on the basics of protein folding and what drives it. The textbooks
aren't likely to be way off base.

"How many proteins are there in humans?
It has been hard enough counting genes. Proteins can be spliced
in different ways and decorated with numerous functional groups,
all of which makes counting their numbers impossible for now."

Nonsense. We make less than 100,000 different proteins and probably
less than 50,000. There's no great mystery here.

"How do proteins find their partners?
Protein-protein interactions are at the heart of life. To
understand how partners come together in precise orientations
in seconds, researchers need to know more about the cell's
biochemistry and structural organization."

It's relatively simple second order kinetics. What's the problem?

"What roles do different forms of RNA play in genome function?
RNA is turning out to play a dizzying assortment of roles, from
potentially passing genetic information to offspring to muting
gene expression. Scientists are scrambling to decipher this
versatile molecule."

No new roles have been discovered in the past 25 years. Why does anyone
think there are any more than the ones we know about?

"Why are some genomes really big and others quite compact?
The puffer fish genome is 400 million bases; one lungfish's
is 133 billion bases long. Repetitive and duplicated DNA don't
explain why this and other size differences exist."

Of course repetitive DNA doesn't explain this, why should it? Maybe
it's just an accident that some genomes are larger than others. There
doesn't have to be an adaptationist explanation for everything.

"What is all that "junk" doing in our genomes?
DNA between genes is proving important for genome function and
the evolution of new species. Comparative sequencing, microarray
studies, and lab work are helping genomicists find a multitude of
genetic gems amid the junk."

Bull***. Most of the DNA isn't doing anything. That's why it's called
junk.

"How can genome changes other than mutations be inherited?
Researchers are finding ever more examples of this process,
called epigenetics, but they can't explain what causes and
preserves the changes."

We've known about methylation, and understood how it works, for over
35 years. This is one of the main causes of epigenetic inheritance.

"Will there ever be a tree of life that systematists can agree on?
Despite better morphological, molecular, and statistical methods,
researchers' trees don't agree. Expect greater, but not complete,
consensus."

What the hell does this mean? There will never be anything in biology
that achieves "complete" consensus.

"How many species are there on Earth?
Count all the stars in the sky? Impossible. Count all the species
on Earth? Ditto. But the biodiversity crisis demands that we try."

This is one of the top 100 scientific questions?

"What is a species?
A "simple" concept that's been muddied by evolutionary data; a
clear definition may be a long time in coming."

There will never be a "clear" definition. That's the nature of biology
and evolution. Don't these guys get it? Who asked these questions?
Kindergarten students?

Sheesh!



Larry Moran















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