http://www.nnseek.com/e/sci.bio.evolution/ Posts for sci.bio.evolution Fri, 26 Dec 2008 10:02:02 PST http://www.nnseek.com/ http://www.nnseek.com/img/64.png 64 64 NNSeek http://www.nnseek.com/e/sci.bio.evolution/nanotechnology_in_cancer_treatment_113081602t.html http://www.nnseek.com/e/sci.bio.evolution/nanotechnology_in_cancer_treatment_113081602t.html opportunity to study and interact with normal and cancer cells in real
time, at the molecular and cellular scales, and during the earliest
stages of the cancer process. Through the concerted development of
nanoscale devices or devices with nanoscale materials and components,
the NCI Alliance for Nanotechnology in Cancer will facilitate their
integration within the existing cancer research infrastructure.

http://bioisolutions.blogspot.com/2008/12/nanotechnology-in-cancer.html

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]]> Fri, 26 Dec 2008 10:02:02 PST http://www.nnseek.com/e/sci.bio.evolution/news_origin_of_life_on_earth_simple_fusion_to_jump_113041410t.html http://www.nnseek.com/e/sci.bio.evolution/news_origin_of_life_on_earth_simple_fusion_to_jump_113041410t.html ScienceDaily (Dec. 23, 2008) - With the aid of a straightforward experiment,
researchers have provided some clues to one of biology's most complex
questions: how ancient organic molecules came together to form the basis of
life.

Specifically, this study demonstrated how ancient RNA joined together to
reach a biologically relevant length.

RNA, the single-stranded precursor to DNA, normally expands one nucleic base
at a time, growing sequentially like a linked chain. The problem is that in
the primordial world RNA molecules didn't have enzymes to catalyze this
reaction, and while RNA growth can proceed naturally, the rate would be so
slow the RNA could never get more than a few pieces long (for as nucleic
bases attach to one end, they can also drop off the other).

Ernesto Di Mauro and colleagues examined if there was some mechanism to
overcome this thermodynamic barrier, by incubating short RNA fragments in
water of different temperatures and pH.

They found that under favorable conditions (acidic environment and
temperature lower than 70 degrees Celsius), pieces ranging from 10-24 in
length could naturally fuse into larger fragments, generally within 14
hours.

The RNA fragments came together as double-stranded structures then joined at
the ends. The fragments did not have to be the same size, but the efficiency
of the reactions was dependent on fragment size (larger is better, though
efficiency drops again after reaching around 100) and the similarity of the
fragment sequences.

The researchers note that this spontaneous fusing, or ligation, would a
simple way for RNA to overcome initial barriers to growth and reach a
biologically important size; at around 100 bases long, RNA molecules can
begin to fold into functional, 3D shapes.

Journal reference:

1.. Samanta Pino, Fabiana Ciciriello, Giovanna Costanzo and Ernesto Di
Mauro. Nonenzymatic RNA ligation in water. J. Biol. Chem, DOI:
10.1074/jbc.M805333200
Adapted from materials provided by American Society for Biochemistry and
Molecular Biology, via EurekAlert!, a service of AAAS.

American Society for Biochemistry and Molecular Biology (2008, December 23).
Origin Of Life On Earth: Simple Fusion To Jump-start Evolution.
ScienceDaily. Retrieved December 25, 2008, from
http://www.sciencedaily.com/releases/2008/12/081218213634.htm
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Robert Karl Stonjek

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]]> Thu, 25 Dec 2008 23:07:03 PST http://www.nnseek.com/e/sci.bio.evolution/rna_world_problem_113041154t.html http://www.nnseek.com/e/sci.bio.evolution/rna_world_problem_113041154t.html googlemail.com> wrote:
> Hi Tom,
>
> On Dec 19, 7:03=3DA0am, "Tom Hendricks" att.net> wrote:
>
>
>
> > 1. Life began as the most stable chemical reaction to the environment
> > (stable in both keeping what works and altering what needed fixing for =
mo=3D
> re
> > stability)
> > 2. The environment that was most likely on earth during the origin was =
ho=3D
> t
> > with the bombardment phase turning the oceans to steams more than once.=
I=3D
> t
> > also had heavy bombardment of UV radiation from a weaker sun.
>
> Early Earth likely hosted a multitude of physico-chemical environments
> and micro-environments -- many of them likely to fluctuate in time.
> Temperature cycles in an RNA world environment are plausible as well
> as
> up-concentration of reactants due to thermal effects (e.g. evaporation
> or freezing
> of solvent).
>
> > Hot environment has some very positive aspects to it - hot speeds up
> > chemical processes, hot would suggest a PCR type environmentally forced
> > replication of RNA strands, =3DA0hot gets results like the Miller - Ure=
y
> > experiments.
>
> The following links might be of interest for you:
>
> Non-enzymatic nucleic acid polymerization and replication:http://flint.sd=
u.dk/research/polymerization.html
>
> and
>
> Does the RNA-World Still Retain its Appeal After 40 Years of
> Research?http://www.springerlink.com/content/n355000830941242/
> in case you have access to scientific journals.
>
> - harold -

What time are we talking about here?
And remember we had the UV problem till about 2.5.bya

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]]> Thu, 25 Dec 2008 23:07:03 PST http://www.nnseek.com/e/sci.bio.evolution/news_life_got_bigger_in_two_million_fold_leaps_scientists_113040898t.html http://www.nnseek.com/e/sci.bio.evolution/news_life_got_bigger_in_two_million_fold_leaps_scientists_113040898t.html > "The fossil record indicates pretty clearly that you need a eukaryotic cell
> to make that first size jump," Payne said. "It isn't just that the bacteria
> don't get there as fast, it is that bacteria still haven't gotten there 1.6
> billion years later.

The two jumps idea is fascinating. But I would like to comment on
something else.
Bacteria are not on a mission to get anywhere. The reason they haven't
changed is
because what they were doing was so well adapted to the environment.
It's the rest of life that has had problems that forced continual
change.
I think we should look at life as about 99%% bacteria on a successful
road that
has little changed, and a small offshoot of life that is in flux to
fit the environment.

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]]> Thu, 25 Dec 2008 23:07:03 PST http://www.nnseek.com/e/sci.bio.evolution/news_life_got_bigger_in_two_million_fold_leaps_scientists_113040642t.html http://www.nnseek.com/e/sci.bio.evolution/news_life_got_bigger_in_two_million_fold_leaps_scientists_113040642t.html bigpond.net.au> wrote:
> Life got bigger in two, million-fold leaps, scientists say
> December 22nd, 2008 in Space & Earth science / Earth Sciences
>
[snip]

> "All of the oxygen in the atmosphere ultimately exists because of the
> evolution of cyanobacteria," Payne said. "Plants that produce oxygen today
> during photosynthesis, their ability to do that is ultimately derived from
> cyanobacteria."
>
[snip]

This seems to answer the question I raised here recently but only got
one (partial) answer to. The origin of atmospheric oxygen was
photosynthesis. This is certainly what Christian de Duve says in his
1995 book 'Vital Dust'.

Anthony Campbell

--
Anthony Campbell - ac@acampbell.org.uk
Microsoft-free zone - Using Debian GNU/Linux
http://www.acampbell.org.uk (blog, book reviews,
and sceptical articles)

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]]> Thu, 25 Dec 2008 23:07:03 PST http://www.nnseek.com/e/sci.bio.evolution/uv_absorbance_difference_between_purines_and_pyrim_112519938t.html http://www.nnseek.com/e/sci.bio.evolution/uv_absorbance_difference_between_purines_and_pyrim_112519938t.html http://matcmadison.edu/biotech/resources/methods/labManual/unit_4/exercise_15.ht...

"Most biological molecules do not intrinsically absorb light in the visible range, but they do absorb ultraviolet light. Biologists take advantage of UV absorbance to quickly estimate the concentration and purity of DNA, RNA, and proteins in a sample... It is also possible to quantify the amount of DNA in a sample by looking at its absorbance at a wavelength of 260nm or 280nm (in the UV region)...

Proteins have two absorbance peaks in the UV region, one between 215-230 nm, where peptide bonds absorb, and another at about 280 nm due to light absorption by aromatic amino acids (tyrosine, tryptophan and phenylalanine). Certain of the subunits of nucleic acids (purines) have an absorbance maximum slightly below 260 nm while others (pyrimidines) have a maximum slightly above 260 nm. Therefore, although it is common to say that the absorbance peak of nucleic acids is 260 nm, in reality, the absorbance maxima of different fragments of DNA vary somewhat depending on their subunit composition. "

What if UV is a selective force at the start of life. If purines, and pyrimidines have slightly different absorbance maximums, then wouldn't each have a selective advantage under certain UV conditions?

Thoughts?

Tom Hendricks

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]]> Tue, 16 Sep 2008 09:34:16 PDT http://www.nnseek.com/e/sci.bio.evolution/informational_genetics_112519170t.html http://www.nnseek.com/e/sci.bio.evolution/informational_genetics_112519170t.html
``Informational genetics refers to the unification of Shannon's
information theory and genetics.''

- http://alife.co.uk/essays/informational_genetics/
--
__________
|im |yler http://timtyler.org/ tim@tt1lock.org Remove lock to
reply.

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]]> Tue, 16 Sep 2008 09:34:16 PDT http://www.nnseek.com/e/sci.bio.evolution/news_cells_from_space_have_unusual_makeup_112304130t.html http://www.nnseek.com/e/sci.bio.evolution/news_cells_from_space_have_unusual_makeup_112304130t.html
Sept. 8, 2008
Special to World Science

A lineage of odd microbes that may have crashed into Earth aboard a meteor
in 2001 seem to contain molecules not found in Earthly cells, two scientists
are reporting.

Although many remain skeptical over the remarkable claim of minuscule
extraterrestrial visitors, Godfrey Louis, head of the physics department at
Cochin University of Science and Technology in India, presented the findings
at a scientific conference in San Diego on Aug. 12.

The meeting was organized by SPIE, the International Society for Optical
Engineering. The acronym reflects its former name as Society of
Photo-Optical Instrumentation Engineers.

The microbes give off unsual sorts of fluorescence under specific lighting
conditions, which follow patterns never seen in normal cells, according to
Louis and Santhosh Kumar of Mahatma Gandhi University in India, co-authors
of the report. The likely explanation, they added, is that the particles
contain molecules not found in Earthly organisms.

Louis and Kumar previously reported that the odd particles contain no DNA,
although they replicate abundantly in ferocious heat by spawning new "cells"
from within themselves. It was these offspring whose fluorescence properties
the pair tested.

Mysterious, tiny red globules fell to Earth in a red rain that pelted parts
of southern India sporadically for about two months in 2001, causing
widespread puzzlement. The event, however, was the latest in a series of
reports of colored rains from various places stretching back centuries, some
better documented than others.

Louis and Kumar say the orbs could be cells from space because they have
biological characteristics but match no known life form. A space rock could
have broken up in the atmosphere and seeded clouds with these organisms, the
pair argues, citing witness reports of an airburst just before the showers.
Other scientists have conceded the particles are mystifying, but the claim
of live cells from space is so bizarre that many are holding back any
assent.

Some note that the hazards of journey through space, including intense
radiation and extraordinary travel times, make the possibility of bacterial
transfer among different solar systems unlikely.

"Exchanges of bacteria between planets in different solar systems are only
possible during the birth cluster stage of the systems," when they're
situated close together in a star cluster, wrote scientists with NASA and
other institutions in a report this month. Our own solar system is far from
being in such a stage. That paper has been accepted for publication in the
research journal Astrophysical Journal Letters.

On the other hand, researchers with Kristianstad University in Sweden and
other institutions reported on Sept. 8 that some tiny Earth animals called
tardigrades proved surprisingly resilient in outer space. Dried-out
tardigrades lived for 10 days unprotected in that environment, and went on
to reproduce, these scientists wrote in the Sept. 9 issue of the research
journal Current Biology.

Louis and Kumar are persisting in their studies; their ideas have gained
support from figures such as Chandra Wickramasinghe, director of the Cardiff
Centre for Astrobiology at Cardiff University, U.K.

In his presentation, Louis said that "red cell" spawns under various
lighting conditions exhbited properties violating a scientific principle
known as Kasha's Rule, found to have few exceptions elsewhere. The rule has
to do with fluorescence, the phenomenon in which a substance emits light of
one color upon stimulation by light from another color. Kasha's rule holds
that in general, the color of the arriving light and the emitted light are
unrelated.

To the contrary, Louis found that in the red globules' "offspring," alone
among cells on Earth, these colors are related by a distinct pattern.

"Hence the presence of new kind of bio-molecules can be inferred," Louis
wrote in the presented paper. "Organisms replicating at 300 degrees
[Celsius] and showing this kind of autofluorescence are currently unknown to
exist on earth yet several thousand kilograms of these cells came down
through the red rain." The original parent cells are also under fluorescence
testing and results will be reported later, Louis said.

Source: World Science
http://www.world-science.net/exclusives/080908_redrain

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Robert Karl Stonjek

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]]> Thu, 11 Sep 2008 09:28:04 PDT http://www.nnseek.com/e/sci.bio.evolution/paper_understanding_the_limits_to_generalizability_112303874t.html http://www.nnseek.com/e/sci.bio.evolution/paper_understanding_the_limits_to_generalizability_112303874t.html 31 January 2008; Accepted 5 June 2008


Understanding the limits to generalizability of experimental evolutionary
models
Samantha E. Forde 1,5, Robert E. Beardmore 2,5, Ivana Gudelj 2,3,5, Sinan S.
Arkin 2, John N. Thompson 1 & Laurence D. Hurst 4

1.. Department of Ecology and Evolutionary Biology, University of
California, Santa Cruz, California 95064, USA
2.. Department of Mathematics, Imperial College London, London SW7 2AZ, UK
3.. Department of Mathematical Sciences and,
4.. Department of Biology & Biochemistry, University of Bath, Bath BA2
7AY, UK
5.. These authors contributed equally to this work.

Abstract:
Given the difficulty of testing evolutionary and ecological theory in situ,
in vitro model systems are attractive alternatives; however, can we appraise
whether an experimental result is particular to the in vitro model, and, if
so, characterize the systems likely to behave differently and understand
why? Here we examine these issues using the relationship between phenotypic
diversity and resource input in the T7-Escherichia coli co-evolving system
as a case history. We establish a mathematical model of this interaction,
framed as one instance of a super-class of host-parasite co-evolutionary
models, and show that it captures experimental results. By tuning this
model, we then ask how diversity as a function of resource input could
behave for alternative co-evolving partners (for example, E. coli with
lambda bacteriophages). In contrast to populations lacking bacteriophages,
variation in diversity with differences in resources is always found for
co-evolving populations, supporting the geographic mosaic theory of
co-evolution. The form of this variation is not, however, universal. Details
of infectivity are pivotal: in T7-E. coli with a modified gene-for-gene
interaction, diversity is low at high resource input, whereas, for
matching-allele interactions, maximal diversity is found at high resource
input. A combination of in vitro systems and appropriately configured
mathematical models is an effective means to isolate results particular to
the in vitro system, to characterize systems likely to behave differently
and to understand the biology underpinning those alternatives.

Source: Nature
http://www.nature.com/nature/journal/v455/n7210/abs/nature07152.html

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]]> Thu, 11 Sep 2008 09:28:04 PDT http://www.nnseek.com/e/sci.bio.evolution/call_for_abstracts_spatial_evolutionary_dynamics_112303618t.html http://www.nnseek.com/e/sci.bio.evolution/call_for_abstracts_spatial_evolutionary_dynamics_112303618t.html Please kindly help forward it to potentially interested colleagues and
students.

SPATIAL EVOLUTIONARY DYNAMICS WORKSHOP
Institut des Systemes Complexes (ISC), Paris, October 17, 2008
This workshop addresses the special features of evolutionary dynamics
that occur in explicitly spatial models compared with traditional mean
field models.

The aim is to bring together scientists studying the effects of
spatial extent ("isolation by distance") and configuration on
evolutionary dynamics. Authors are invited to submit a 1-page abstract
on their research, or on a review and discussion about any aspect of
spatial evolutionary dynamics. Contributions may be original or
already published (please specify when submitting).

Keynote speaker: Paulien Hogeweg <http://www-binf.bio.uu.nl/ph>
Organizing committee: Guy Hoelzer <http://www.scsr.nevada.edu/~bioweb/
hoelzer.html> and Rene Doursat <http://doursat.free.fr>
Workshop Website: http://www.iscpif.fr/SED2008

Overview
Evolutionary theory remains largely entrenched in the lessons of
mathematical models assuming well-mixed populations, or sets of
subpopulations without any spatial configuration (the so-called
"island model" of migration), which cannot exhibit the emergence of
spatial pattern or its influence on evolutionary rates. However, these
behaviors have been routinely observed in spatially explicit
computational models of the evolutionary process (usually agent-based)
developed in recent years, and they represent general aspects of
complex systems theory.

This is a very important trend for evolutionary theory as
diversification of types is the central concept of evolutionary
biology. Darwin established this as the core idea of evolution with
the title of his book on "the origin of species". Now is an ideal time
to identify and characterize the spatially explicit computational
modeling approach for understanding the evolutionary process. There
have been over 100 papers published exploring spatially explicit
computational evolution models, which appear to present a consistent
message revealing inadequacies of neo-Darwinistic mean-field models
and calling for a new understanding of spatio-temporal evolutionary
dynamics. For example, extending models of evolving populations in one
or more spatial dimensions seems to frequently (always?) tend toward
spatial self-organization (population subdivision/speciation) and
enhance ecological and social adaptation (including the evolution of
cooperation). We hope that interactions during this workshop will help
to clarify which aspects of traditional evolutionary theory are
generally challenged by these models.

To give an example, here is a link to a recent paper by the organizers
exploring parapatric speciation in the absence of environmental
influences:

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000126

CALL FOR ABSTRACTS
Important Dates:
Deadline for abstract submission: Tuesday, September 30
Notification of acceptance: Friday, October 3
Abstracts should be submitted electronically by email addressed to
both organizers: Guy Hoelzer ( hoelzer[AT]unr.edu ) and Rene Doursat
( rene.doursat[AT]polytechnique.edu ).
The number of speakers is limited to 12 and the total number of
attendees to 35.
Submissions will be reviewed based on their relevance to the workshop,
clarity, and overall quality.
If you only want to attend without giving a presentation, please
notify the organizers by email.
There is no registration fee for this workshop.

TOPICS OF INTEREST
While we anticipate that most presentations will describe particular
models and their behavior, contributions and viewpoints about the
following topics are especially encouraged:

Similarities and differences in modeling approaches and assumptions.
Similar and dissimilar outcomes (behaviors) of alternative spatially
explicit evolutionary models or empirical examples.
To what extent do our efforts represent a major paradigm shift for
evolutionary biology. If this is a significant paradigm shift, then
how do we most effectively communicate the new perspective to
colleagues during the transition?
What role should traditional mean-field theory of population genetics
play in the future?
For example, is it sufficient for most circumstances in the same sense
that Newtonian models generally suffice even after the theory has been
superseded by general relativity?
Alternatively, the mean-field models may be too error prone under most
circumstances, recommending wholesale replacement by spatially
explicit models.
Can we begin to prescribe a framework to guide the development of
future spatially explicit computational models of evolution?
While we, as colleagues, may recognize commonalities and categories
among our models, they often appear to be disconnected and
idiosyncratic to evolutionary biologists trained to recognize more
traditional types of models. It could be very useful if we could
begin to agree upon a consistent terminology for categorizing the new
forms of models in computational evolution. This might help others to
more easily see the theoretical threads connecting various
computational models, thus facilitating a more rapid appreciation for
the depth of this new perspective.
Finally, what possible transfers and applications could be created
toward artificial evolution of spatially distributed devices?

Program
The details of the program will be announced once we have a list of
scientists interested in presenting at the workshop. All speakers will
be asked to give relatively brief (around 30mn) presentations about
their models and/or views about such models. The workshop will
conclude with a round table discussion aiming to characterize this
body of research and its future prospects.

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]]> Thu, 11 Sep 2008 09:28:04 PDT