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  Topic: Science Break, Selected Shorts< Next Oldest | Next Newest >  
Richardthughes



Posts: 11178
Joined: Jan. 2006

(Permalink) Posted: Nov. 16 2010,13:49   

E-coli solves suduku

http://www.newscientist.com/article....ku.html

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
sledgehammer



Posts: 533
Joined: Sep. 2008

(Permalink) Posted: Nov. 16 2010,16:33   

Quote (Richardthughes @ Nov. 16 2010,11:49)
E-coli solves suduku

http://www.newscientist.com/article....ku.html

From the article:  
Quote
"If you consider an ant colony, an individual ant isn't very useful," he told New Scientist. "But if you put millions of ants together they're suddenly capable of very rich, very complex population-level behaviour. That's what we're trying to harness."

Something Sal will, apparently, never understand.

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The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
ppb



Posts: 325
Joined: Dec. 2006

(Permalink) Posted: Nov. 17 2010,07:56   

Quote (Richardthughes @ Nov. 16 2010,14:49)
E-coli solves suduku

http://www.newscientist.com/article....ku.html

So, if you're working on a tough Sudoku puzzle, it's best to go with your gut.

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"[A scientific theory] describes Nature as absurd from the point of view of common sense. And it agrees fully with experiment. So I hope you can accept Nature as She is - absurd."
- Richard P. Feynman

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Nov. 17 2010,17:06   

One pot OOL synthesis - formamide to RNA

The money shot:
Quote
The production in the same chemical frame of acyclonucleotides (Saladino et al. 2003), the abiotic phosphorylation of nucleosides to yield cyclic nucleotides (Costanzo et al. 2007), their nonenzymatic polymerization to yield long RNA chains (Costanzo et al. 2009), and the non-enzymatic terminal ligation of oligomers (Pino et al. 2008; Costanzo et al. 2009) show that the whole series of events leading from a one-carbon atom precursor (NH2COH) to RNA polymers may be accomplished within a single chemical frame.



Big shout out of thanks to NASA for the virtual OOL workshop (read about it on PT). Many fantastic lectures available online.

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Nov. 22 2010,15:09   

Bone Marks - By Design or By Chance?

Homework question - why haven't these scientists used the Explanatory Filter?

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Nov. 22 2010,16:55   

Quote (dvunkannon @ Nov. 22 2010,14:09)
Homework question - why haven't these scientists used the Explanatory Filter?

They did use it, but then they flushed and went back to the lab to do some more work.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Nov. 23 2010,12:46   

Quote (dvunkannon @ Nov. 22 2010,16:09)
Bone Marks - By Design or By Chance?

Homework question - why haven't these scientists used the Explanatory Filter?

More data for the Explanatory Filter to filter

Apparently, these elephants mining salt in a cave on Mt Elgon in Kenya fooled some 19th century biologists about the origin of the marks on the wall of the cave. Did they use the Explanatory Filter to correct themselves?

(Since the elephants visit the cave at night, direct observation of how the marks were made was difficult.)

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Nov. 23 2010,13:24   

Quote
Homework question - why haven't these scientists used the Explanatory Filter?


No.

EF can only be used to discern the work of imaginary entities having no attributes.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Nov. 23 2010,13:36   

What could be more natural than applying the Explanatory Filter to the 9-11 Truth Movement? Building 7, was the collapse natural or designed? Come on, DDr.. Dembski, the accolades of an entirely new wing of the wingnut universe is waiting for the answer...

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Nov. 23 2010,16:26   

Quote (Henry J @ Nov. 22 2010,16:55)
 
Quote (dvunkannon @ Nov. 22 2010,14:09)
Homework question - why haven't these scientists used the Explanatory Filter?

They did use it, but then they flushed and went back to the lab to do some more work.

flushed? I'd have thought they should have blushed.

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Rocks have no biology.
              Robert Byers.

  
Henry J



Posts: 5786
Joined: Mar. 2005

(Permalink) Posted: Nov. 23 2010,21:52   

Quote
flushed? I'd have thought they should have blushed.

Hey, I didn't say what they used it for! ;)

Henry

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Nov. 24 2010,12:22   

Quote (Henry J @ Nov. 23 2010,21:52)
 
Quote
flushed? I'd have thought they should have blushed.

Hey, I didn't say what they used it for! ;)

Henry

LOL...

--------------
Rocks have no biology.
              Robert Byers.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Nov. 24 2010,13:10   

DNA = Quantum Computers?

Some 2010 papers on that...

DNA Replication via Entanglement Swapping

The relevance of continuous variable entanglement in DNA

Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effect

EDIT - fixed title of third paper

  
Richardthughes



Posts: 11178
Joined: Jan. 2006

(Permalink) Posted: Nov. 30 2010,10:59   

Place your bets on the forthcomming NASA press conference:

http://kottke.org/10/11/has-nasa-discovered-extraterrestrial-life

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Nov. 30 2010,11:09   

Quote (Richardthughes @ Nov. 30 2010,10:59)
Place your bets on the forthcomming NASA press conference:

http://kottke.org/10/11/has-nasa-discovered-extraterrestrial-life

Quote
Update: According to Alexis Madrigal, the answer to the hyperbolic question in the headline is "no".

I'm sad to quell some of the @kottke-induced excitement about possible extraterrestrial life. I've seen the Science paper. It's not that.


--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
REC



Posts: 638
Joined: Sep. 2006

(Permalink) Posted: Nov. 30 2010,11:34   

Exciting! My guess is they found something "weird" here on earth.

Felisa Wolfe-Simon and Steven Benner are authors on a paper outlining the search for weird life and shadow biospheres-life on earth we wouldn't easily recognize as life. Something without DNA, or ribosomes, something not sharing common ancestry with the rest of life.

James Elser fits this too, as a biogeologist.

Davies, P. C. W. , Benner, S.A., Cleland, C.E., Lineweaver,C.H., McKay,C.P. and Wolfe-Simon, F. Signatures of a Shadow Biosphere (2009) Astrobiology. 9(2): 241-249.

doi:10.1089/ast.2008.0251.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Nov. 30 2010,11:37   

I like this summary for my guess.

Interesting findings which support the possibility the origin of life could have been extraterristial.

EDIT- Kudos to Richard for posting this.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Nov. 30 2010,16:01   

Quote (Thought Provoker @ Nov. 24 2010,13:10)
DNA = Quantum Computers?

Some 2010 papers on that...

DNA Replication via Entanglement Swapping

The relevance of continuous variable entanglement in DNA

Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effect

EDIT - fixed title of third paper

Interesting papers; thanks for the links!

However, I'm not sure what they have to do with quantum computers. They describe how quantum effects may be important in base pairing, replication, & duplex stability. I don't see the relevance to quantum computing, other than perhaps "computing" which bases should pair with one another.

  
keiths



Posts: 2195
Joined: Jan. 2006

(Permalink) Posted: Nov. 30 2010,18:47   

Quote
Complexity not so costly after all, analysis shows

ANN ARBOR, Mich.—The more complex a plant or animal, the more difficulty it should have adapting to changes in the environment. That's been a maxim of evolutionary theory since biologist Ronald Fisher put forth the idea in 1930.

But if that tenet is true, how do you explain all the well-adapted, complex organisms—from orchids to bower birds to humans—in this world?

This "cost of complexity" conundrum puzzles biologists and offers ammunition to proponents of intelligent design, who hold that such intricacy could arise only through the efforts of a divine designer, not through natural selection.

A new analysis by Jianzhi "George" Zhang and coworkers at the University of Michigan and Taiwan's National Health Research Institutes reveals flaws in the models from which the cost of complexity idea arose and shows that complexity can, indeed, develop through evolutionary processes. In fact, a moderate amount of complexity best equips organisms to adapt to environmental change, the research suggests. The findings will be published online in the Proceedings of the National Academy of Sciences during the week of Sept. 27.


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And the set of natural numbers is also the set that starts at 0 and goes to the largest number. -- Joe G

Please stop putting words into my mouth that don't belong there and thoughts into my mind that don't belong there. -- KF

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Nov. 30 2010,19:01   

Qetzal,

Quantum computers are good at searching unsorted databases.  From Wikipedia...
   
Quote
Grover's algorithm is a quantum algorithm for searching an unsorted database with N entries in O(N1/2) time and using O(log N) storage space (see big O notation). It was invented by Lov Grover in 1996.

In models of classical computation, searching an unsorted database cannot be done in less than linear time (so merely searching through every item is optimal). Grover's algorithm illustrates that in the quantum model searching can be done faster than this; in fact its time complexity O(N1/2) is asymptotically the fastest possible for searching an unsorted database in the quantum model.

Dembski's No Free Lunch argument is based on the presumption of an unsorted search using classical algorithms.  Quantum computing does what is impossible classically.

In 2001, Apoorva D. Patel wrote a paper titled Quantum algorithms and the genetic code
Quote
Over the last few years, Grover's algorithm has been studied in detail. I just summarise some of the important features:
...
 The algorithm is known to be optimal [10], going from |s> to |b> along a geodesic. No other algorithm, classical or quantum, can locate the desired object in an unsorted database with a fewer number of queries.
 The iterative steps of the algorithm can be viewed as the discretised evolution of the state vector in the Hilbert space, governed by a Hamiltonian containing two terms, |b> <b| and |s> <s|. The former represents a potential energy attracting the state towards |b>, while the latter represents a kinetic energy diffusing the state throughout the Hilbert space. The alteration between Ub and Us in the discretised steps is reminiscent of Trotter’s formula used in construction of the transfer matrix from a discretised Feynman’s path integral [11].
...
With the use of superposition of all possibilities at the start, the quantum algorithm performs a directed walk to the final result and achieves the square-root speed-up.
 The result in eq. (3) depends only on |<b|s>|; the phases of various components of |s> can be arbitrary, i.e. they can have the symmetry of bosons, fermions or even anyons.

To come back to the genetic code, let us look at two of the solutions of eq. (3) for small Q. The only exact integral solution is Q = 1,N = 4. Base-pairing during DNA replication can be looked upon as a yes/no query, either the pairing takes place through molecular bond formations or it does not, and its task is to distinguish between 4 possibilities. The other interesting solution is Q = 3, N = 20:2. The well-known triplet code of DNA has 3 consecutive nucleotide bases carrying 21 signals [12], 20 for the amino acids plus a STOP [13]. 3 base-pairings between t-RNA and m-RNA transfer this code to the amino acid chain [5].

These solutions are highly provocative. This is the first time they have come out of an algorithm that performs the actual task accomplished by DNA. It is fascinating that they are the optimal solutions [14]. Indeed it is imperative to investigate whether DNA has the quantum hardware necessary to implement the quantum search algorithm.

Patel's observation was mostly disregarded because the concept of the "quantum hardware necessary" existing in a biological environment was just too incredible to accept without more empirical evidence.

A lot has changed since 2001, especially lately which is why the three papers I linked to were something I noticed.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Nov. 30 2010,19:54   

Thought Provoker,

Sorry, I still don't see how any of that suggests that DNA is any sort of quantum computer.

BTW, we discussed that Patel paper in a previous thread. I can't speak to the math, but the biochemistry & molecular biology are incredibly wrong. Makes it hard for me to take any of the rest seriously.

  
Richardthughes



Posts: 11178
Joined: Jan. 2006

(Permalink) Posted: Dec. 01 2010,11:57   

http://scienceblogs.com/startsw....bui.php

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Dec. 02 2010,13:12   

http://www.nasa.gov/multimedia/nasatv/index.html

Live

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Dec. 04 2010,16:06   

The abstract of Speculation on Quantum Mechanics and the Operation of Life Giving Catalysts
Quote
The origin of life necessitated the formation of catalytic functionalities in order to realize a number of those capable of supporting reactions that led to the proliferation of biologically accessible molecules and the formation of a proto-metabolic network. Here, the discussion of the significance of quantum behavior on biological systems is extended from recent hypotheses exploring brain function and DNA mutation to include origins of life considerations in light of the concept of quantum decoherence and the transition from the quantum to the classical. Current understandings of quantum systems indicate that in the context of catalysis, substrate-catalyst interaction may be considered as a quantum measurement problem. Exploration of catalytic functionality necessary for life’s emergence may have been accommodated by quantum searches within metal sulfide compartments, where catalyst and substrate wave function interaction may allow for quantum based searches of catalytic phase space. Considering the degree of entanglement experienced by catalytic and non catalytic outcomes of superimposed states, quantum contributions are postulated to have played an important role in the operation of efficient catalysts that would provide for the kinetic basis for the emergence of life.


Magnetism, FeS colloids, and Origins of Life is freely available on-line.  It includes...
Quote
Today, clear signatures of quantum processing in biology are coming in ((Engel et al. 2007), aided by femtosecond laser-based 2D spectroscopy and coherent control approaches, showing how phase relationships in nano-structures modulate the course of bio-reactions (Nagya et al 2006). As to decoherence evading mechanisms, the role of a gel-state; quasicrystalline order; (Jibu et al 1994; Hagan et al. 2002); are amongst proposed order maintaining mechanisms in a wet environment, while 'screening effect', or 'cocooning' structural mechanisms are seen as providing insulation against interactions with the environment [Patel (2001); Davies (2003, 2004)] (see also Sect. 3.9). Indeed, it seems that Nature has quietly been using these strategies all along, i.e. leading to creation of biological language itself, as the Grover-Patel search numbers match those used by Nature! Using Grover's quantum search method for a marked item in an unsorted database, Patel (2001) hit upon the base-pairing logic of nucleic acids in transcription and translation as an excellent quantum search algorithm { a directed walk through a superposition of all possibilities - resulting in a 2-fold increase in sampling efficacy over its classical counterpart (which at best permits a random walk).
...
This possibility seems intriguing in the light of Patel's findings, where quantum searches seem to be responsible for the creation of biological language itself. Moreover, Russell et al have argued that life's hatchery could have been busy by 3.8 Gyr, evolving fast enough for a branch to have reached the ocean surfaces by 3.5 Gyr, as evidenced by photosynthetic signatures. The gestation period of life had to have been less than the umbilical mound's delivery of the formative hydrothermal solution, i.e., certainly less than 3 million years, and probably less than 30,000 years (Fruh-Green et al. 2003). Indeed, a magnetic start to Life could provide the ingredients for an intelligent Ancestor, along the lines envisaged by Lloyd (2006) for a computing universe. Again, it seems to be a physically feasible embodiment (Mitra-Delmotte and Mitra 2007; 2009) of Paul Davies's Q-Life proposal (2008), as also acknowledged by him in Merali (2007). A magnetic basis of assembly could also offer robustness to an `open' system against interference from a decohering environment. On the other hand, as evidence of quantum processing effects in biology trickles in, it appears that Nature is equipped for tackling environmental intrusion.

I linked to this paper over at Telic Thoughts but I doubt anyone is going to run with it as a Pro-ID argument.

Let me know if you are tired of arguing with JoeG and others like him and I will post a thread and try to defend the concepts offered by this paper.

  
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Dec. 09 2010,17:47   

http://www.newscientist.com/blogs....go.html

World's oldest computer recreated in Lego

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
sledgehammer



Posts: 533
Joined: Sep. 2008

(Permalink) Posted: Dec. 09 2010,20:22   

Evolution Texts Survive Challenge in Louisiana
John Roach writes: The theory of evolution has survived the latest attack in the struggle to insert creationism-flavored themes into science classrooms.
On Tuesday, a committee of Louisiana's school board recommended in a 6-to-1 vote that the state approve purchase of industry-standard textbooks on evolution, which have been attacked by Christian conservatives for failing to teach the "controversy" about evolution.

"That sent a strong signal from the Louisiana board of education that they want accurate science taught in the classrooms, and that publishers don't need to put in these creationists' critiques," Joshua Rosenau, the programs and policy director of the National Center for Science Education, told me.

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The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
Wesley R. Elsberry



Posts: 4991
Joined: May 2002

(Permalink) Posted: Dec. 10 2010,05:46   

The Worms Turn... and a Patient Recovers

My take on a CNN article about an ulcerative colitis patient self-medicating with Trichuris trichuria nematodes.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Richardthughes



Posts: 11178
Joined: Jan. 2006

(Permalink) Posted: Dec. 13 2010,16:11   

http://www.technologyreview.com/blog/arxiv/26132/?ref=rss

Astronomers Find Evidence Of Other Universes In Cosmic Microwave Background

ID will not pleased.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Albatrossity2



Posts: 2780
Joined: Mar. 2007

(Permalink) Posted: Dec. 13 2010,16:17   

Adult stem cells take on a whole new level of meaning. Stem cells derived from liposuctioned fat could be used for breast augmentation, replacing silicone implants.

Gordon Mullings, GEM of Talky, will not be pleased.

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Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Schroedinger's Dog



Posts: 1692
Joined: Jan. 2009

(Permalink) Posted: Dec. 13 2010,16:17   

Quote (Richardthughes @ Dec. 13 2010,22:11)
http://www.technologyreview.com/blog/arxiv/26132/?ref=rss

Astronomers Find Evidence Of Other Universes In Cosmic Microwave Background

ID will not pleased.

[head explodes]

Beside that, I've always been convinced that our universe is just one bubble in the large cup of moccaccino some fat ass is sipping down in Xxtrublub.

Take a look at a cup of hot coffee.

I mean, have you ever really looked at your hand?!?




Ok, I think it's time for me to go to sleep...

--------------
"Hail is made out of water? Are you really that stupid?" Joe G

"I have a better suggestion, Kris. How about a game of hide and go fuck yourself instead." Louis

"The reason people use a crucifix against vampires is that vampires are allergic to bullshit" Richard Pryor

   
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