human origin

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#85
Jan 31, 2013
 
In comparison, for
evolution on fitness landscapes one typically obtains a
distribution / 1/t corresponding to a sampling of waiting
times for passing over barriers [19,20], although a
1/t2 distribution can be obtained by supplementing a hill
climbing concept with the assumption that extinction of a
given species is determined by evolutionary rates of older
species [21]. Abandoning fitness landscapes, the ecological
network model of ref.[22,23] instead determines the
fate of a species through an ecological connectivity matrix.
When this evolving network of species is assigned
a connectivity that is comparable to (eco)system size, it
shows a 1/t2 distribution of genera lifetimes. In contrast
to these macro-evolutionary models, our study of
Boolean networks only considers one species, with a comparison
to species extinction data that is based on an
extrapolation of the obtained evolutionary clock.
In conclusion we have studied evolution of Boolean networks
in absence of any competition. This simplification
allowed us to discuss how the requirement of evolving robust
networks in itself may lead to an evolution which
exhibits punctuated equilibrium.
ACKNOWLEDGMENTS
S.B. thanks NORDITA, Copenhagen, for kind support
and warm hospitality and the Deutsche Forschungsgemeinschaft
for funding this work.
[1] C. Darwin, The Origin of Species by Means of Natural
Selection (Penguin, Harmondsworth, 1968).
[2] S. Wright, Evolution 36, 427 (1982).
[3] M. Kimura, The Neutral Theory of Molecular Evolution
(Cambridge University Press, Cambridge, U.K., 1983).
[4] C.M. Newman, J.E. Cohen, and C. Kipnis, Nature 315,
400 (1985).
[5] R. Lande, Proc. Natl. Acad. Sci. U.S.A. 82, 7641 (1985).
[6] S.J. Gould and N. Eldredge, Nature 366, 223 (1993).
[7] P. Schuster, J. Weber, W. Gruner, and C. Reidys, in
Physics of Biological Systems: From Molecules to Species
edited by H. Flyvbjerg et al.(Springer Verlag, Berlin,
1997).
[8] P. Bak and K. Sneppen, Phys. Rev. Lett. 71, 4083 (1993).
[9] M. Ptashne, A Genetic Switch, Phage Lambda and
Higher Organisms (Cell Press & Blackwell Scientific Publications,
Oxford, U.K., 1992).
[10] S.A. Kauffman, J. Theor. Biol. 22, 437 (1969).
[11] R. Somogyi and C.A. Sniegoski, Complexity 1(6), 45-63
(1996).
[12] J.A. de Sales, M.L. Martins, and D.A. Stariolo, Phys.
Rev. E 55, 3262 (1997).
[13] D. Thieffry and R. Thomas, in Pacific Symposium on
Biocomputing 98 edited by R.B. Altman et al. 3, 77
(1998) and “http:// www.smi.stanford.edu/ projects/
helix/ psb98/ thieffry.pdf”.
[14] S.A. Kauffman, Physica D 42, 135 (1990).
[15] R. Somogyi and S. Fuhrman, in Proc. of the International
Workshop on Information Processing in Cells and
Tissues (1997), in press and “http:// rsb.info.nih.gov/
mol-physiol/ reprints/ Distributivity.pdf”.
[16] L. Van Valen, Evolutionary Theory 1, 1 (1973).
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#86
Jan 31, 2013
 
http://arxiv.org/pdf/physics/9708026.pdf
Bornholdt. 1998

The post that did not appear might however magically still pop up but the article is interesting to read in full.

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#87
Jan 31, 2013
 
http://www.guardian.co.uk/science/punctuated-...

Avians developed together with their sex-chromosomes.
jumping genes Barbara McClintock
quote:
You may recall that I recently wrote about retroposons, often referred to in the mainstream media as "jumping genes".

Retroposons are repetitive DNA fragments that are sprinkled throughout the genome. They are copied ("reverse transcribed") from an RNA intermediary that randomly "jumps" to another locus within the genome where they insert themselves. The original repetitive retroposon sequence identities and locations are inherited like other genetic loci, but the new insertion locations (along with any changes in sequence) are unique and are reliably inherited from the time they are inserted. The resulting patterns of change are easy to see and can be followed through ensuing generations for more than 100 million years -- major evolutionary timescales. In short, retroposons are molecular fossils.

Like other chromosomes, sex chromosomes carry retroposons. Since similar genes (gametologues) on the avian Z and W chromosomes are not swapping genetic information, their evolution can be mapped by the presence or absence of retroposons (figure 1):

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#89
Jan 31, 2013
 
But have the genes located on the sex chromosomes evolved similarly to each other? And what does the pattern of sex chromosome evolution tell us about the evolution of birds?

You may recall that I recently wrote about retroposons, often referred to in the mainstream media as "jumping genes".

Retroposons are repetitive DNA fragments that are sprinkled throughout the genome. They are copied ("reverse transcribed") from an RNA intermediary that randomly "jumps" to another locus within the genome where they insert themselves. The original repetitive retroposon sequence identities and locations are inherited like other genetic loci, but the new insertion locations (along with any changes in sequence) are unique and are reliably inherited from the time they are inserted. The resulting patterns of change are easy to see and can be followed through ensuing generations for more than 100 million years -- major evolutionary timescales. In short, retroposons are molecular fossils.

Like other chromosomes, sex chromosomes carry retroposons. Since similar genes (gametologues) on the avian Z and W chromosomes are not swapping genetic information, their evolution can be mapped by the presence or absence of retroposons (figure 1):

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#90
Jan 31, 2013
 
Figure 1.
DOI: 10.1093/molbev/msr147

The above diagramme shows how a pair of gametologues change as retroposed elements (REs) insert into each member of the pair at different times. The large gray boxes are exons (genes), small gray boxes are untranslated regions (not encoding any proteins), and the white boxes are retroposons [figure 1, larger view].

The gene on the left represents the pair whilst they were crossing over frequently. At that point, they look the same. However, after recombination stops, these regions on the sister chromosomes are free to diverge independently along their own evolutionary pathways, giving rise to two very similar, but no longer identical, gametologues (right side). REs that inserted prior to the cessation of crossing over (asterix) are inherited by both gametologues, whilst those REs that "jumped" after crossing over ceased (circle) are unique to just one of the gametologues. Of course, the corresponding regions of the two gametologues are different lengths, too.

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#92
Jan 31, 2013
 
Not surprisingly, a different tree topology was obtained for NIPBL, because recombination ceased independently in this gene pair in the neoavian and in the galloanseran lineage (figure 2b; larger view). Unfortunately, it's not clear from the DNA data whether recombination ceased in the ancestor of Galloanserae or shortly after they diverged.

The gene tree of ATP5A1 is quite complex. It looks as though recombination ceased independently in all six neoavian representatives that were included in this study (figure 2c; larger view), but more study and more avian representatives are necessary to better understand these patterns and when they occurred.

"We have looked at sex chromosome evolution in birds from a perspective based on rare genomic changes," writes Mr Suh in email.

As I already mentioned, retroposon insertions are very useful for uncovering evolutionary relationships. But this new study shows yet another use of retroposons: helping us to understand the temporal sequence of sex chromosome evolution and gametolog differentiation. By tracing the pattern of RE insertions in gametologues of living bird species, it is possible to follow this back to the common ancestor of their sex chromosomes.

"To our knowledge, this has not been done in any other sex chromosomal system yet -- so it should be promising to have a look at the many other sex chromosomal systems (e.g., in mammals, snakes, some turtles, some fish, some plants) from this perspective."

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#95
Jan 31, 2013
 
Margulis SET
http://cpsbiology.blogspot.nl/2008/09/evoluti...
On the evolution of eukaryotic cells.

I choose the blogspot because it gives more insights, points to ponder.

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#96
Feb 2, 2013
 
Also links to tools as IEEE and mega 5
http://mbe.oxfordjournals.org/content/23/11/2...

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#97
Feb 2, 2013
 

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#98
Feb 2, 2013
 
Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

e-mail: jafarsharif@rcai.riken.jp
Abstract
Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.

retrotransposons intracisternal A particles DNA methylation environmental cues adaptive response
Footnotes
One contribution of 15 to a Theme Issue ‘Mammalian epigenetics in biology and medicine’.
© 2012 The Author(s) Published by the Royal Society. All rights reserved.

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#99
Feb 2, 2013
 
hmmm i suppose the next step would be some short definitions of nuclease and protease.
A popular article on how a virus affected humanity becoming human.
And about elicitation given that the beauty industry is conserving plants but sells hellishly expensive products that according to me and some scientist simply can't reach the sites/depth where they could be effective. So a double entendre.

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#100
Feb 2, 2013
 
nuclease /nu·cle·ase/(noo´kle-&#257 ;s) any of a group of enzymes that split nucleic acids into nucleotides and other products.

See wiki

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#101
Feb 2, 2013
 
Protease Digestive Enzyme to help digest proteins.

See wiki

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#102
Feb 2, 2013
 
Did Viruses Make Us Human?
By Kathy A. Svitil|Friday, November 01, 2002
Around 6 million years ago, some unknown genetic changes caused chimpanzees and humans to diverge from a common ancestor and set off along very different evolutionary paths. John McDonald, a molecular evolutionist at the University of Georgia, attributes this split to a most unlikely trigger—bits of "junk" DNA that we probably inherited from ancient viruses.

The human genome is littered with scraps of DNA that serve no clearly defined function. Scientists believe these transposons—so called because they can jump around the chromosomes—were acquired millions or billions of years ago, when viruses inserted their own DNA into that of the host. Until recently, transposons were regarded as genetic junk. But when geneticists discovered that the junk accounts for nearly half of our genome, "people started to seriously consider that they might contribute to evolution," McDonald says.

McDonald and King Jordan from the National Institutes of Health in Bethesda, Maryland, have now bolstered that view. They looked at one family of 147 related transposons, called HERV-K elements, and compared them in several different primate species. A single HERV-K element is present in humans but not in chimps. Judging from other measures of genetic change, this transposon appeared 6 million years ago, exactly when humans and chimps went their separate ways. McDonald hypothesizes that bits of viral DNA might have inserted themselves and altered functional genes, modifying the proteins they make, or the viral bits might have incited a reshuffling of the primate genome. "We like to think that our DNA must be serving us, but the vast majority of our genome is not directly related to our own function. We are carrying sequences that serve only the DNA. We're just part of a larger picture," McDonald says.

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#103
Feb 2, 2013
 
Viruses can f.i. also embed in the RNA, or be seen as selfish or 'junk-DNA' but after 10,000 to 35,000 generations can become a deterrent to attacks of other virusses of the same sort.
So beneficial.

relative fitness-reproductive value.

fitness-genetic contribution to the individuals and it;s decendents continued life.

https://docs.google.com/viewer...

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#104
Feb 2, 2013
 
ERV's endegenous retroviruses (iin DNA) and why they are called like that.
And what they do
The newyorker. Darwins surprise.

http://www.dailygalaxy.com/my_weblog/2008/08/...

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#105
Feb 2, 2013
 
Codons and anti-codons work together to form proteins.

Further relevant terms and short explanations of the processes involved.

http://www.experts123.com/q/how-do-codons-and...

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#106
Feb 2, 2013
 
An example how elicitation works.
basicly the stem-cells of plants are activated and enforced in a lab. this can be done by various techniques.

This text explains the process and f.i. the use of UV light.
http://webcache.googleusercontent.com/search...

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#107
Feb 2, 2013
 
From the FBI site (we would call it phishing f.i.)

Why Elicitation Works

A trained elicitor understands certain human or cultural predispositions and uses techniques to exploit those. Natural tendencies an elicitor may try to exploit include:

■A desire to be polite and helpful, even to strangers or new acquaintances
■A desire to appear well informed, especially about our profession
■A desire to feel appreciated and believe we are contributing to something important
■A tendency to expand on a topic when given praise or encouragement; to show off
■A tendency to gossip
■A tendency to correct others
■A tendency to underestimate the value of the information being sought or given, especially if we are unfamiliar with how else that information could be used
■A tendency to believe others are honest; a disinclination to be suspicious of others
■A tendency to answer truthfully when asked an “honest” question
■A desire to convert someone to our opinion
For example, you meet someone at a public function and the natural getting-to-know-you questions eventually turn to your work. You never mention the name of your organization. The new person asks questions about job satisfaction at your company, perhaps while complaining about his job. You may think,“He has no idea where I work or what I really do. He’s just making idle chat. There’s no harm in answering.” However, he may know exactly what you do but he relies on his anonymity, your desire to be honest and appear knowledgeable, and your disinclination to be suspicious to get the information he wants. He may be hunting for a disgruntled employee who he can entice to give him insider information.

Techniques

There are many elicitation techniques, and multiple techniques may be used in an elicitation attempt. The following are descriptions of some of those techniques.

Assumed Knowledge: Pretend to have knowledge or associations in common with a person.“According to the computer network guys I used to work with…”

Bracketing: Provide a high and low estimate in order to entice a more specific number.“I assume rates will have to go up soon. I’d guess between five and 15 dollars.” Response:“Probably around seven dollars.”

Can you top this? Tell an extreme story in hopes the person will want to top it.“I heard Company M is developing an amazing new product that is capable of …”

Confidential Bait: Pretend to divulge confidential information in hopes of receiving confidential information in return.“Just between you and me…”“Off the record…”

Criticism: Criticize an individual or organization in which the person has an interest in hopes the person will disclose information during a defense.“How did your company get that contract? Everybody knows Company B has better engineers for that type of work.”

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#108
Feb 2, 2013
 
Deliberate False Statements / Denial of the Obvious: Say something wrong in the hopes that the person will correct your statement with true information.“Everybody knows that process won’t work—it’s just a DARPA dream project that will never get off the ground.”

Feigned Ignorance: Pretend to be ignorant of a topic in order to exploit the person’s tendency to educate.“I’m new to this field and could use all the help I can get.”“How does this thing work?”

Flattery: Use praise to coax a person into providing information.“I bet you were the key person in designing this new product.”

Good Listener: Exploit the instinct to complain or brag, by listening patiently and validating the person’s feelings (whether positive or negative). If a person feels they have someone to confide in, he/she may share more information.

The Leading Question: Ask a question to which the answer is “yes” or “no,” but which contains at least one presumption.“Did you work with integrated systems testing before you left that company?”(As opposed to:“What were your responsibilities at your prior job?”)

Macro to Micro: Start a conversation on the macro level, and then gradually guide the person toward the topic of actual interest. Start talking about the economy, then government spending, then potential defense budget cuts, then “what will happen to your X program if there are budget cuts?” A good elicitor will then reverse the process taking the conversation back to macro topics.

Mutual Interest: Suggest you are similar to a person based on shared interests, hobbies, or experiences, as a way to obtain information or build a rapport before soliciting information.“Your brother served in the Iraq war? So did mine. Which unit was your brother with?”

Oblique Reference: Discuss one topic that may provide insight into a different topic. A question about the catering of a work party may actually be an attempt to understand the type of access outside vendors have to the facility.

Opposition/Feigned Incredulity: Indicate disbelief or opposition in order to prompt a person to offer information in defense of their position.“There’s no way you could design and produce this that fast!”“That’s good in theory, but…”

Provocative Statement: Entice the person to direct a question toward you, in order to set up the rest of the conversation.“I could kick myself for not taking that job offer.” Response:“Why didn’t you?” Since the other person is asking the question, it makes your part in the subsequent conversation more innocuous.

Questionnaires and Surveys: State a benign purpose for the survey. Surround a few questions you want answered with other logical questions. Or use a survey merely to get people to agree to talk with you.

Quote Reported Facts: Reference real or false information so the person believes that bit of information is in the public domain.“Will you comment on reports that your company is laying off employees?”“Did you read how analysts predict…”

Ruse Interviews: Someone pretending to be a headhunter calls and asks about your experience, qualifications, and recent projects.



Target the Outsider: Ask about an organization that the person does not belong to. Often friends, family, vendors, subsidiaries, or competitors know information but may not be sensitized about what not to share.

Volunteering Information / Quid Pro Quo: Give information in hopes that the person will reciprocate.“Our company’s infrared sensors are only accurate 80% of the time at that distance. Are yours any better?”

Word Repetition: Repeat core words or concepts to encourage a person to expand on what he/she already said.“3,000 meter range, huh? Interesting.”

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