Tuesday, April 27, 2021

https://www.quikly.com/carls-jr/s/lWzkBjpV?utm_content=blogger

Monday, February 12, 2018

#TheScienceOf Internet Trolls



#TheScienceOf Internet Trolls (video by Scientist Mel)
+Scientist Mel Excellent video and I think it is something perhaps we all need to be reminded of every so often on how to deal with trolls as they will always be around as it is one of the darker sides of the Internet. Some people just seem to prefer to spend more time trying to tear down others for simply for their own personal entertainment and it's pretty sad in my opinion, but I think we can all take to heart some of the advice you gave in your video...as well as these basic guidelines on how to handle trolls that I think is excellent for the GDC to adopt as guidelines on handling trolls on the Internet.

1. Establish a Policy
2. Ignore Them (by far the best advice)
3. Make Light of the Situation
4. Unmask Them
5. Don’t Provide a Platform
6. Use Moderators and Online Tools
7. Create a Unified Community
8. Listen
9. Fight Back With Facts
10. Correct Mistakes

Types of trolls to determine best course of action. If you see certain types of behavior it may help you to determine what type of troll you're dealing with. I think I have ran into every type of these since I have been in YouTube.
(From Mel's video)

Rabid Flamer Sharing Troll
Grammar Troll Profane Screamer
Cry baby White Knight
Never Give up Expert
Retroactive Stalker Spoiler
Lame Teenager Fraud
Self Feeding Flooder
Bored Hater Lair
Niellie Neggerson Stalker


https://www.forbes.com/sites/johnrampton/2015/04/09/10-tips-to-dealing-with-trolls/#5117ec5c54f4


https://www.youtube.com/watch?v=9OrW0xVr3jQ

Tuesday, January 23, 2018

DNA as a "code' does not mean it was created by an intelligent agent

A 'code" in semiotics is when you have a symbol being replaced by a letter or word (most of time) which is deciphered into a normal readable language...there is nothing about DNA being a "code" that fits that description. Man "arbitrarily" assigned names to the nucleotides based upon what nitrogenous base they have and gave those names a symbol to represent them. Those symbols do not translate into any normal readable language. The calling of DNA a "code" is merely a very loose informal analogy to help students better understand conceptually how DNA to protein synthesis works in the central dogma of biology. Stop trying to use a poor analogy by calling DNA a "code" thinking that it necessitates the existence of a intelligent designer. It doesn't and you're just committing the fallacy of faulty analogy

Wednesday, November 29, 2017

Bloggers and YouTubers "Deflating Atheism" and "Escaping Atheism"

Bloggers and YouTubers "Deflating Atheism" and "Escaping Atheism" (Dean Esmay aka "Max Kolbe": American loon #655 http://americanloons.blogspot.com/2013/08/655-dean-esmay.html)) decided to take a swing (and a miss) at me, Aron Ra, Genetically Modified Skeptic and Godlesss Cranium. (Time stamp 27:30) https://youtu.be/-_Y0mKm1dwo?t=27m30s

https://escapingatheism.com/2017/11/29/deflating-escaping-week-atheist-stupid-twis/

From Max in his comment section:
"We'd argue that McRae is worse. He's one of those scumbags like Penn Jillette who puts on a show of being reasonable but knows exactly what he's doing when he lies his ass off. And Steve McRae never stops lying."


Now let's look at the massive irony here shall we? While I'm sincerely flattered to be compared to Penn Jillette and that I "put on a show of being reasonable" I find it pretty comical that here is a person accusing me of lying and yet makes a video calling me an atheist...after being corrected on this numerous times. As Godless Cranium astutely notes I self Identify as a temporal agnostic, which is not an atheist by more formal definitions. I have never once self identified as an atheist, but here are two theist completely and willfully lying about my theological position in a video deliberately relating me to a ideological position that I do not hold to.

Another interesting thing to note from the video is that neither of them truly seem to understand the word "skeptic" or that it is a polysemous term that represents many possible meanings. The word itself to me is rather vague, as there are many types of skeptics...and generally the word refers to someone to adheres to Skepticism, a philosophical position that I don't have as it maintains that philosophical skepticism questions our ability to make knowledge claims. I am quite fine with make knowledge claims as I have a pretty well defined epistemic framework that allows me to make knowledge claims...now, if one is referring to scientific skepticism then sure, I would be a scientific skeptic who does believe that scientist should be ethical and follow Mertonian norms...but it is quite obvious that neither Deflating Atheism nor Escaping atheism understand these types of positional nuances. They are quite typical of people who focus more on assigning their own version of a label to someone, rather than trying to actually understand that persons beliefs and positions.

I also would very much like to know how I am being paid to "be a skeptic" or how I "make cash" by converting people to atheism. 3 years on YouTube and I know of absolutely no one that I have ever "converted" to atheism...nor of a penny that I have earned from making one either.

Max then goes on to make the infelicitously bizarre claim that I am in an "atheist cult" and that I have a "talking point" of "I hope I have offended you"...in my 570+ videos on YouTube those words have never been uttered by me. My goal on YouTube is not to offend, it is to foster meaningful and interesting dialog between people with various differing positions. Does this mean no one ever gets offended? Of course not...as if someone on YouTube isn't offended by something you say every so often, then you really have nothing of consequence to say.

Thursday, November 23, 2017

Tautologies using metalogic

( Φ ∧  Ψ ) -> Φ and ( Φ ∧ Ψ ) -> φ are tautologies. Why? Since for the same reason that (p ∧ q) -> p as well as (p ∧ q) -> q are tautologies. If you do the truth tables:

(p ∧ q ) -> p

p q p ∧ q (p∧ q) -> p
T T T T
T F F T
F T F T
FF F T

ALL values are TRUE...thus it is a tautology.

Just do the same for (Φ ∧ Ψ ) -> Φ and ( Φ ∧  Ψ ) -> φ as they are also tautologies. Remember these symbols "Φ" and "Ψ" are just symbols that represent other symbols in metalogic. We can substitute (p ∧ q ) -> p and see that is a tautology as all values are T.

(So it is clear you get T for (p ∧ q) ->p by implication, since
p ->q means ¬p V q or here it, (p ∧ q) ->p, means ¬(p∧ q) V p )

Wednesday, October 25, 2017

Regarding the Claims! Claims! Claims! stream and the ternary system.

Regarding the Claims! Claims! Claims! stream and the ternary system.
or ternarinception
-By Barney Tearspell

Regarding the Claims! Claims! Claims! stream and the ternary system.
or ternarinception

Let’s employ some programming skills with ternary operators and a bit of logic and see where it gets us.


-

definitions and notation
Before I get into the argument let me set up some tools. You can skip or glance over these, but they're there if you need them later.

We assume that it is only possible to hold one of three positions on any proposition

A = Accept
B = Reject
C = Abstain

Given any proposition P one can then make three derived propositions P' of the form:

PA ⇔ position on P is 'Accept'
PB ⇔ position on P is 'Reject'
PC ⇔ position on P is 'Abstain'

The ternary system must then be applicable to each of those statements but must retain logical consistency, so each statement must infer meaning about the other statements.

PA ⇔ PAA ∧ PBB ∧ PCB

In other words:
Accepting P is equivalent to Accepting PA AND Rejecting PB AND Rejecting PC

And the relation can be written as:

PAA ⇔ PBB ∧ PCB
Accepting PA is equivalent to Rejecting PB And Rejecting PC
In other words:
Accepting P is equivalent to neither Rejecting nor Abstaining from P


Solving this derived set of propositions gives complete information about the position on P.

This chain of derived statements should hold all the way down to the axioms if the system is to be consistent

-

disagreeing with TheRumpus

+TheRumpus Account has claimed that statements like not-accept are illegal because they lead to contradiction.

I disagree. Statements that are contradictions are illegal, but statements that are not contradictions are fine-just-fine (but might be incomplete).

The way in which this becomes crystal clear for me is to see it from an outsiders perspective trying to find out what some person's position is

So lets write the legal positions.

The set where I agree with TheRumpus

PAA ⇒ PBB ∧ PCB
position is known: the person Accepts P (e.g., Theism)

PBA ⇒ PAB ∧ PCB
position is known: the person Rejects P (e.g., Hard Atheism)

PCA ⇒ PAB ∧ PBB
position is known: the person Abstains on P (e.g., Agnosticism)

Since the position is known, any of these sufficiently answers the question:
“What position does the person hold on P?”


The set TheRumpus calls illegal


¬PAA ⇒ (PBA ∨ PCA)
position is unknown: the person either Rejects or Abstains on P (e.g. non-theism)
Along with PAA, sufficiently answers the question “Does the person Accept P?”
Technically the full form is: ¬PAA ⇒ (PBA ∨ PCA) ∨ (PBC ∧ PCC) but it can be reduced with no loss.

¬PBA ⇒ (PAA ∨ PCA)
position is unknown: the person either Accepts or Abstains on P
Along with PBA, sufficiently answers the question “Does the person Reject P?”
Technically the full form is: ¬PBA ⇒ (PAA ∨ PCA) ∨ (PAC ∧ PCC) but can be reduced with no loss.

¬PCA ⇒ (PAA ∨ PBA)
position is unknown: the person either Accepts or Rejects P
Along with PCA, sufficiently answers the question “Does the person Abstain on P?”
The long form would contain a contradiction in the second part of the statement so that part must be excluded (giving a consistent reduction)

And there are other non-contradictory values in the derivations such as
PAC ∧ PBC ∧ PCC which would reduce to PC but I would argue that it a possible answer in case the person doesn’t know of P (literally, doesn’t know of the proposition itself)

Contrast this with ternary values (T - true, F - false, U - undefined).
A negation of ternary values would work something like:

¬T=F
¬F=T
¬U=U

And applying that to the examples in which this ternary system is proposed, you could get the following exchange:
"Are you an Agnostic?" - "No!" - "Oh, so you're an Agnostic then."

-

Conclusion

All of this violates the excluded middle rule but maps much better to how people actually think (since ignorance is a major component of cognition) and converse.

It could be interesting to derive the mathematical properties and rules of the system and construct truth tables (or rather the position tables) to see how the positions interact and sum up to see which form of ternary logic would fit best.

Tuesday, October 24, 2017

Problem with Divine Command Theory presupper's don't want to address.

Problem with Divine Command Theory presupper's don't want to address.


It was truly enjoyable to watch a presupper creationist run ass in hand when he was trying to question how morality exists with out God by asking:

"So today it might be wrong to kill and eat a three-year-old child but next year in might be perfectly acceptable in your world view right?"

to which I just replied to him the obvious:

"Nothing I said even remotely would imply that...in YOUR world view that would be perfectly acceptable if GOD COMMANDED IT right?

If God commanded you to go out and kill and eat the first 20 babies you found...YOU would have to do it because it was MORAL to you right? So today it may not be moral to you....but tomorrow it may be perfectly moral to you because your GOD COMMANDS YOU TO DO IT!"

He left a few comments later after completing avoiding having to address what I said.

Go figure.

Complementary sets of a universal set.

Given p=theism, then theism is a category, and NOT theism is also a category. The universal category give by a complementary set of A'= U\A where A'={x∈U |x∉A} This means that anything NOT in set A or theism, exists at an element in A' or NOT THEISM which again is the universal set minus the category set of A. Since elements of A are mutually exclusive to A' then any x as a member of A as a member of U can not at same time be member of A', which means p v ~p are mutually exclusive sets as well.

Thoughts?

Colorless green ideas sleep furiously...interpretations of Chomsky's famous statement.

Colorless green ideas sleep furiously...interpretations of Chomsky's famous statement.

Ozymandias Ramses II seems to prefer using the phrase "Colorless green ideas sleep furiously" (or some variation, as I don't remember if that is the "exact" phrase he uses) to describe things which are semantically nonsensical, even if grammatically correct. Usually when discussing things like theological non-cognitivism which would be if someone said that the statement made no sense and therefore could not have a truth value of attached to it...but If one wanted to make that phrase semantically correct, could there be (at least) two ways of doing it?

1) By use of polsemy such that each word has more figurative meaning and can be re-interpreted in some other way, that doesn't change the over all meaning of the word, but only how the contextually or semantically the words operate with in the phrase.

2) Adhere to the Bertrand Russell approach that any sentence that is not true for what ever reason, is false...so if we said colorless green ideas with "ideas" being the operative noun and colorless green just being descriptors then it simple boils down to ideas don't sleep, since ideas are just concepts in a mind, but they do not have the ability to sleep, therefore the sentence is not true and therefore is false. So a propositional value could be attached that sentence. So here a theological non-cog could still attach a F value as the sentence is no longer meaningless to them in the sense of not being able to have a truth value attached to it (even if still semantically nonsensical)... it is just false because it is not true.

Thoughts?

A response I wrote to someone claiming we don't have beliefs, and that beliefs are always without evidence (or little evidence):


A response I wrote to someone claiming we don't have beliefs, and that beliefs are always without evidence (or little evidence):


If I asked a semasiological question "What is the meaning of the word "belief" I am asking what we have sociality attached to it to convey meaning. The way you are using loses that colloquial understanding of the word, as the word "belief" is a very real cognitive state of a person that a propositional state (propositionally) is true (or false), or that something ontologically exists in our universe (metaphysically). It makes no difference if the justification for their belief is evidential, pragmatic, or prudential...or even it is unjustified and lacking warrant.

If I said p=at least one God exists in reality (or p=some God exists, or p=one or more God exists in our universe)

Then if someone is asked to provide a truth value for that proposition, that is a "belief" state. If someone says that T is true (theist) that is a "belief"...REGARDLESS of it being justified or not. If someone says that statement is false (philosphical atheist) that too is a "belief".

Everyone has beliefs, and to resorting to epistemological nihilism is just absurd. If I took a different approach and asked an onomasiological question: "What is the cognitive state when you take a position on a proposition being true or false?" ...we have a word for that...the answer would be "belief".

Thoughts?

Positive vs Negative Claims:

Positive vs Negative Claims:


There seems to be a lot of confusion lately of what constitutes a positive and negative claim...as there does seem to be some vagueness as to what that actually means. A negative claim is often the phrase used when someone expresses that something does not exist, as opposed to claiming that it does exist.

To me if I say X does not exist, that is making a positive claim of the negative existence of something which people call a negative claim, but this leads to confusion. As one is making that claim that the state of affairs of the universe is such that X does not exist in the universe, or the universe is devoid of X.

Personally, I don't care if someone calls this a negative claim or a positive claim...as both require just as much a burden of justification...and I think the distinction is rather meaningless to me.

Again to me, if someone saying "God does not exit", viewed by me, is a positive assertion of a negative claim (claim of nonexistence). Since in a debate both parties are arguing their own positions, both are arguing from a position that their position is correct and both need to give positive evidence for their position (Evidence for their own position), not just negative evidence (evidence against the opponents position)...which to me means both are in essence making a positive claim. Calling something like "God does not exist!" a "negative claim" doesn't mean it has any less of a burden of justification.

Thoughts?

(May have a hangout on this soon as well as that constitutes a claim as +Nesslig 20 and +TheRumpus Account have been going back and forth on this for a while and ofc Rumpus thinks everyone in the world is an idiot, but him. His position is that "I believe God does not exist" ("declaration of belief") is not a claim and is different from saying "God does not exist!" (assertion/claim). Nesslig and I disagree with Rumpus here, as I view it someone saying "I believe God does not exist", while declaring their belief, is making a weak statement that is saying ontologically that the universe is devoid of Gods and I take that as a claim. What are you thoughts?)

Tuesday, December 6, 2016

Reds Rhetoric trolls G-man by calling his cell phone to ask him a very i...

G-man wanting to have his own Atheist Experience like call in show and used his own personal cell phone number so people could call in and ask him questions. Reds Rhetoric decided to ask him live on air the most important question of them all! LIKE this VIDEO if you laughed :)

Music by Fiona Robertson: DarkBeats
(Used by permission)

Free music: Cataclysmic Molten Core

Monday, November 28, 2016

So CR Ministries has decided to make a "Chick tract" like post about me...and like "Chick tracts" they make a completely fallacious argument (as well as get what I do think wrong.)

1) I do think just about everything they put up in their images is seriously lacking in scientific awareness, but promoting a fallacious argument against evolution does not falsify evolutionary theory. We have an evolutionary niche that allows us to have a complex form of linguistic communication...other species have communication as well. Some forms like the pheromone secretion of trees travel miles and miles which is vastly superior to our communication method. Does that make trees more special than us?

2) They assert science is "extremely biased". This is just a subtle way of saying that actual scientists do not want pseudoscience being published in their journals. If young Earth creationists could actually demonstrate just one of their claims truly indicated a young Earth, they would be taken seriously. They can't...and they aren't.

3) I am not certain that the universe is 14+ billion year old...I am however certain that the best current estimate we have place it around 13.77 billion year old ±.059 bya. Not a major fubbery of course, but still shows that CR ministries doesn't really know even what the actual modern consensus is for the age of the universe.

4) I do not believe life was created by happenstance, and nowhere have I ever made such a claim. I believe life is governed by very complex physics and chemical reactions, along with an emergent properly we call consciousness.

5) I too believe life was designed, in fact it is an important discovery by Charles Darwin that life could have been teleonomically designed by nature...and the evidence does tend to support teleonomic design rather than a teleological design. But that does not mean either one is not possible, and it would be nearly (perhaps even totally) impossible to distinguish one from the other.

6) Dawkins admits things appear to be designed, because to him as a biologist things are designed...but by nature, not by an Intelligent Designer. "Appearance" of design is just that, an "appearance". Random waves from the ocean can make very complex intricate wave patterns along the beach, but that does not mean an intelligent force was behind them...or even the formation of a snowflake can be thoroughly explained by physics and meteorology, no reason to invoke an intelligent agent. Many things that were a mystery 200 years age, are now explained by science. The "Intelligent Design" argument is really nothing more than a veiled God of the Gaps argument than actual science.

Thoughts?

Friday, October 28, 2016

Clinton's Classified EmailGate investigation "reopened" by FBI...Scandal...




11 days to the election and the FBI has "reopened" their investigation into Hillary Clinton's mishandling of classified information via Blackberry's using her personal private email server containing secret and top secret classified information.

An initial FBI investigation determined that Clinton was "extremely careless" but no criminal charges were filed...even though Clinton expressly denied ever sending classified material via her private server (which was not authorized to hold classified information) the FBI investigation determined that Clinton personally wrote 104 out of the 2,100 email recovered.

Today James Comey, Director of the Federal Bureau of Investigation announced that new emails in connect to an unrelated case may also have contained classified formation and that those emails are now currently under investigation.

I have said many times that this scandal was not over and that the investigation into this scandal was far from over...the questions now are will it have any effect on Clinton's presidential run and if she wins are will we already be starting off her new term quagmired by controversy and political scandal...perhaps even federal crimes? How does this relate to the recent release of information on this by Wikileaks...or does it? So she be held accountable? Why has she been "except" so far when there are at least a dozen other people that have gone to jail and/or fined for far less offenses in mishandling of classified information? Remember Sandy Berger? Fined $50,000 w/2 years probation and stripped of his security clearance for removing files from the National Archives and lying about it? Or Maj. Jason Brezler being discharged from the marines for sending classified information using his private email server?

Three federal laws Clinton may have broken:

Executive Order 13526 and 18 U.S.C Sec. 793(f) of the federal code make it unlawful to send of store classified information on personal email in addition to the Federal Records Act and the State Department’s Foreign Affairs Manual regarding records management.

Section 1236.22 of the 2009 National Archives and Records Administration (NARA).

Violation of the Freedom Of Information Act (FOIA)

I am opening up a room for POLITICAL TALK today...so what do you all think about this new bombshell announcement?

Wednesday, October 26, 2016

Genesis 5 Math as Heilsgeschichte

Here is a visual demonstration regarding Methuselah's "age" of 969, that it's not a real age, since it is the sum total of all the first 17 triangle numbers (between 1 and 153). Note that 153 is the number of fish caught by the disciples when they were having difficulty and the resurrected Christ helped them, in John 21. You can see it in the following table and looking at the table explains what a triangle number is as well:

1
3 = 1+2
6 = 1+2+3
10 = 1+2+3+4
15 = 1+2+3+4+5
21 = 1+2+3+4+5+6
28 = 1+2+3+4+5+6+7
36 = 1+2+3+4+5+6+7+8
45 = 1+2+3+4+5+6+7+8+9
55 = 1+2+3+4+5+6+7+8+9+10
66 = 1+2+3+4+5+6+7+8+9+10+11
78 = 1+2+3+4+5+6+7+8+9+10+11+12
91 = 1+2+3+4+5+6+7+8+9+10+11+12+13
105 = 1+2+3+4+5+6+7+8+9+10+11+12+13+14
120 = 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15
136 = 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16
153 = 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17

969 (adding up the sum total of all the triangle numbers)

Therefore, 153 is a resurrection number in and of itself, where if you do:

1x1x1 = 1
5x5x5 = 125
3x3x3 = 27

Therefore, 1 + 125 + 27 = 153 again!

So, Methuselah's "age" hints at the coming (resurrected) Messiah. This is all that is really going on here, and these "ages" have hidden numeric (and even in this case) prophetic meanings, and therefore are not literal. For more information, check out: Genesis 5 Math as Heilsgeschichte

Tuesday, October 25, 2016

DNA and "higher temperature" -
General Han Solo

In regards to this statement about DNA and a "higher temperature" that nullifies abiogenesis, I advise that TE takes a look at the recent findings of DNA surviving reentry through the Earth's atmosphere:

"Functional Activity of Plasmid DNA after Entry into the Atmosphere of Earth Investigated by a New Biomarker Stability Assay for Ballistic Spaceflight Experiments" - http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0112979.PDF

Most curious is this statement on page 18:

Due to the spin of the payload during ascent and the circular application of the samples, all application sites were equally exposed to high temperatures of up to 118°C. Additionally, the DNA was exposed to temperatures between 80–100°C during the microgravity phase and up to 130°C during ascent and descent phase. The random exposure of the samples to the constantly high temperatures weakens the phosphodiester bond which leads to hydrolysis resulting in single and double strand breaks. The temperature induced DNA damage could explain the different degrees of degradation visible in the agarose gel electrophoration. Futhermore, it is likely that sample quantities are partially reduced during the landing procedure when the payload is landing on ice and snow. Compared to the sample application directly onto the payload surface, small niches in the grooves of the screw heads provided a certain degree of protection against maximum temperatures, and we observed the highest degree of protection on the bottom side. However, intact DNA was detectable for all sample application sites. We therefore conclude that the minimal protection given by the grooves on the surface of the payload structure, as well as by the grooves of the screw heads combined with the observed relatively thick layer (21 mm) of DNA and salt crystals was sufficient for at least a fraction of the DNA molecules to stay intact and retain their full function. The protective role of so called biofilms have been already shown for spores. Additionally, high salt concentration can have a beneficial effect on DNA denaturation and degradation. Salts like MgCl2 and KCl counteract the denaturation of double-stranded DNA at high temperature, and renaturation of single-stranded products of thermodegradation is favoured when the temperature of the incubation mixture decreases. A protective effect of salt crystals for the survival of bacteria under vacuum and UV conditions were reported also earlier. The fact that DNA is susceptible to high temperature was already shown by several groups before. Chiter and colleagues who analysed the transfer of genetic modified organisms in form of DNA fragments could show that temperatures above 95°C for more than five minutes lead to a high level of DNA fragmentation so that it is unlikely that genetic information is retained.

For further information, this was discussed by Dr. Fazale Rana on this podcast recording: http://www.reasons.org/podcasts/apologia-free/dna-can-survive-reentry-from-space
DNA in an aqueous solution-
General Han Solo

Here's a 2013 study that was done in literally visualizing DNA in an aqueous solution because the aqueous solution helped the visualization. Here's the abstract:

The DNA double helix was first elucidated by J.D. Watson and F.H.C. Crick over a half century ago. However, no one could actually “see” the well-known structure ever. Among all real-space observation methods, only atomic force microscopy (AFM) enables us to visualize the biologically active structure of natural DNA in water. However, conventional AFM measurements often caused the structural deformation of DNA because of the strong interaction forces acting on DNA. Moreover, large contact area between the AFM probe and DNA hindered us from imaging sub-molecular-scale features smaller than helical periodicity of DNA. Here, we show the direct observation of native plasmid DNA in water using an ultra-low-noise AFM with the highly sensitive force detection method (frequency modulation AFM: FM-AFM). Our micrographs of DNA vividly exhibited not only overall structure of the B-form double helix in water but also local structures which deviate from the crystallographic structures of DNA without any damage. Moreover, the interaction force area in the FM-AFM was small enough to clearly discern individual functional groups within DNA. The technique was also applied to explore the synthesized DNA nanostructures toward the current nanobiotechnology. This work will be essential for considering the structure–function relationship of biomolecular systems in vivo and for in situ analysis of DNA-based nanodevices.

And here's the conclusion of this excellent study:

We used FM-AFM to directly visualize the double helix structure of plasmid DNA in an aqueous solution. The major and minor grooves between the sugar phosphate backbones of B-DNA were differentiated, and periodic corrugations corresponding to individual phosphate groups in the DNA backbones were resolved. We determined the AFM tip radius as 1.0 nm by comparing the simulated AFM images assuming various tip radii with the FM-AFM image, and the interpretation of the experimental results was validated by the precise comparison of the cross-sectional profiles on the DNA backbones. In addition, we used FM-AFM to perform high-resolution imaging of DNA tiles in an aqueous solution, which showed the righthandedness of B-DNA in the tile and the two different connecting configurations. The results demonstrate the applicability of AFM to sub-molecular-scale investigations of correlations between the structures and functions of DNA under physiological conditions. For example, the approach may allow determination of the structures of various protein nucleic acid complexes or reveal the mechanisms of sequence recognition by DNA-binding proteins. Finally, it should be noted that the technique presented here is one of the most promising analytical tools for investigating the structures of self-assembled DNA nanostructures, such as DNA tiles and DNA origami, which are being developed for applications in DNA computing and other DNA-based nanoscale devices that use the structures and functions of DNA in solution.

Here's the link: https://drive.google.com/open?id=0B1gMXJ3-ViIgQk80WW5zNzNiZ3c

And to top it off, here's an entire PhD dissertation titled, "On the Structure of DNA in an Aqueous Solution" that was published in 1980!

The abstract is as follows:

This thesis deals with the structure of DNA under a variety of conditions of concentration, ionic strength, and association with proteins. I have investigated the behavior of rod-like DNA under conditions of high DNA concentration and low counterion concentration. I have found that the DNA forms specific aggregates, each consisting of seven monomers. Electric dichroism revealed that the conformation of the DNA changes upon formation of these aggregates, with the base tilt angle changing from 17(DEGREES) to 0(DEGREES). I have prepared restriction fragments of DNA and, by combining translational and rotational hydrodynamic data, I have deduced that the diameter of DNA in solution is 24 (+OR-) 2 (ANGSTROM), and the helical rise per residue is 3.15 (+OR-) 0.15 (ANGSTROM). To facilitate analysis of hydrodynamic data, I have developed a technique to measure rotational frictional coefficients of macroscopic objects. I have confirmed the standard equations for cylinders of axial ratio greater than ten, and have developed a relation which is accurate for cylinders of axial ratio down to one. I have developed new equations for the rotation of discs, and I have shown that large perturbations in the draining properties of the object have only a small effect on the frictional coefficient. I have used hydrodynamic measurements to deduce size parameters for the chromatin thick fiber. I have concluded that, in high salt conditions, the thick fiber is 340 (+OR-) 20 (ANGSTROM) thick, with 7-8 nucleosomes per turn. Finally, I have studied the effect of histone H1 on the structure of the nucleosome. I have found that H1 causes some compaction, without much altering the path of the DNA. H1 has an effect on the low salt transition to an unfolded form, but it does not eliminate the transition.

Here's the link: https://drive.google.com/open?id=0B1gMXJ3-ViIgTkxhUmVUTTBqNFU

Sunday, October 16, 2016