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Board Mechanics

AE Public Forum - Fri, 2014-01-17 21:58
Post by fnxtr
Couldn't reach PT at 1:50PST today.
Categories: AE Public BB

Thread for Phoodoo

AE Public Forum - Fri, 2014-01-17 18:12
Post by Friar Broccoli
Quote (Alan Fox @ Jan. 17 2014,10:47)Hi Friar Broccoli

I'm not sure if there is a probationary period. Couple of options. Find an existing thread with a similar topic heading and post in that.

Post it in this thread and I or one of the regulars can set up a thread for you. The thread with the most recent comment comes to the top of the topic list so it should be visible for a while.

Thanks.  As you can see, things seem to be working ok now.
Categories: AE Public BB

MHC/HLA immune genome mutation rates question

AE Public Forum - Fri, 2014-01-17 18:06
Post by Friar Broccoli

I am trying to write up a shorter and clearer (so creationists can read it) version of Lenny Flank's argument about mutation rates as implied by the number of alleles in the MHC complex.  I also want this rewrite because (among other things) the creationist response focuses on his use "beneficial" mutations. (See: )

In my first draft I began:

MHC regions are usually less than 2000 bp long in a genome that is 3,000,000,000 bp long.

Observationally we know there are a 100 mutations per generation over the entire genome.

Therefore in a region that is:

- 300,000,000 bp long we would expect one mutation per generation.
- 3,000,000 bp long we would expect one mutation ever 100 generations.
- 3,000 bp long we would expect one mutation ever 100,000 generations.

Since we sometimes see more than 1000 mutations (alleles) in the 2,000 bp long MHC immune complexes this suggests these areas have been mutating for 100,000,000 generations.

Here I said to myself 100,000,000 generations seems like way too many, unless (for example the mouse MHC complex looks fairly similar - does it?).  If it does not, what is a more reasonable estimate of the number of generations to achieve the diversity we see in the human MHC complexes?

Also is the observed generation to generation rate of mutations in the MHC complexes much different from that observed in the rest of the human genome?
Categories: AE Public BB

Thread for Phoodoo

AE Public Forum - Fri, 2014-01-17 16:47
Post by Alan Fox
Hi Friar Broccoli

I'm not sure if there is a probationary period. Couple of options. Find an existing thread with a similar topic heading and post in that.

Post it in this thread and I or one of the regulars can set up a thread for you. The thread with the most recent comment comes to the top of the topic list so it should be visible for a while.
Categories: AE Public BB

Thread for Phoodoo

AE Public Forum - Fri, 2014-01-17 16:23
Post by Friar Broccoli
I just registered hoping to be able to ask a question here.  But when I try "new topic" in: Discussion Board > From the Panda's Thumb > After the Bar Closes

(the only place that seems active) I get the message:
"Sorry, you do not have permission to start a topic in this forum. You are currently logged in as Friar Broccoli"

What do I need to do?

it's a slightly technical question about counting generations based on mutation rates.
Categories: AE Public BB

Project Steve: n > 1300

With the addition of Stefan Roitsch on January 15, 2014, NCSE's Project Steve attained its 1300th signatory.

Categories: Pro-Science News

A Separate Thread for Gary Gaulin

AE Public Forum - Thu, 2014-01-16 21:23
Post by JohnW
Quote (Alan Fox @ Jan. 16 2014,12:05)Assuming the board has the right info - Happy Birthday to Gary!
Happy birthday*, Gary!

* assuming the planet you live on has a 365.24-day year...
Categories: AE Public BB

Antiscience bill in Oklahoma

Senate Bill 1765 (document), styled the Oklahoma Science Education Act, is the second antiscience bill of the year. As is increasingly common with antiscience legislation, SB 1765 would, if enacted, in effect encourage science teachers with idiosyncratic opinions to teach anything they pleased — proponents of creationism and climate change denial are the usual intended beneficiaries of such bills — and discourage responsible educational authorities from intervening.

Categories: Pro-Science News

Ayala joins NCSE board of directors

Francisco J. Ayala

NCSE is pleased to announce the addition of Francisco J. Ayala, a distinguished evolutionary geneticist at the University of California, Irvine, to its board of directors. 

Categories: Pro-Science News

Quantum effects confirmed for photosynthesis

ARN ID Update - Wed, 2014-01-15 13:12

Quantum phenomena in biology are receiving the attention of more and more researchers, with photosynthesis being the process getting the most attention. Back in 2007, it was apparent that quantum effects were effective for "explaining the extreme efficiency of photosynthesis". Then, in 2010, the photosynthetic apparatus of cryptophyte algae was the focus of research, because its pigments are farther apart than was expected for efficient functioning. In a News & Views article in Nature, van Grondelle & Novoderezhkin discussed evidence suggesting that a process known as quantum coherence is part of the explanation. They added: "This is the first time that this phenomenon has been observed in photosynthetic proteins at room temperature, rather than at much lower temperatures, bolstering the idea that quantum coherence influences light harvesting in vivo." The most recent study has provided a theoretical argument that quantum effects must be present and that classical physics does not provide an explanation. It is claimed to be "the first unambiguous theoretical evidence of quantum effects in photosynthesis". The Press Release describes the work in this way:

"Often, to observe or exploit quantum mechanical phenomena, systems need to be cooled to very low temperatures. This however does not seem to be the case in some biological systems, which display quantum properties even at ambient temperatures. Now, a team at UCL have attempted to identify features in these biological systems which can only be predicted by quantum physics, and for which no classical analogues exist. "Energy transfer in light-harvesting macromolecules is assisted by specific vibrational motions of the chromophores," said Alexandra Olaya-Castro (UCL Physics & Astronomy), supervisor and co-author of the research. "We found that the properties of some of the chromophore vibrations that assist energy transfer during photosynthesis can never be described with classical laws, and moreover, this non-classical behaviour enhances the efficiency of the energy transfer."" (Source here)

New frontiers for understanding the natural world
(image source here)

Most light-gathering macromolecules are composed of chromophores (the light-absorbing pigments) attached to proteins. These are responsible for the first step of photosynthesis, which is to capture light and transfer its energy to another system that can store it. Earlier work showed that energy is transferred in a wave-like manner (the quantum coherence model). However, theoreticians were of the opinion that classical physics could still find a way of explaining the observations.

"Molecular vibrations are periodic motions of the atoms in a molecule, like the motion of a mass attached to a spring. When the energy of a collective vibration of two chromophores matches the energy difference between the electronic transitions of these chromophores a resonance occurs and efficient energy exchange between electronic and vibrational degrees of freedom takes place. Providing that the energy associated to the vibration is higher than the temperature scale, only a discrete unit or quantum of energy is exchanged. Consequently, as energy is transferred from one chromophore to the other, the collective vibration displays properties that have no classical counterpart. The UCL team found the unambiguous signature of non-classicality is given by a negative joint probability of finding the chromophores with certain relative positions and momenta. In classical physics, probability distributions are always positive." (Source here)

Bear in mind that considerable resources have already been spent on trying to develop a biomimetic system that captures solar energy like plants - only to find that photosynthesis is extraordinarily complex and the research has not yet delivered any commercial outputs. It is a reminder that the Darwinian vision of ultimate simplicity has been repeatedly falsified. Photosynthesising microorganisms are among the earliest to appear in the Precambrian fossil record - and yet these organisms have chemical and physical pathways that are only beginning to be understood within the research community. What is emerging are processes and structures that carry the hallmarks of design, with complex specified information at every level of analysis. We are at the beginning of a journey into quantum effects in biology. It is the design paradigm that is best equipped to guide our thoughts and keep us on the right path.

"Other biomolecular processes such as the transfer of electrons within macromolecules (like in reaction centres in photosynthetic systems), the structural change of a chromophore upon absorption of photons (like in vision processes) or the recognition of a molecule by another (as in olfaction processes), are influenced by specific vibrational motions. The results of this research therefore suggest that a closer examination of the vibrational dynamics involved in these processes could provide other biological prototypes exploiting truly non-classical phenomena." (Source here)

Some would want to add neuroscience to this list (see here and here).

Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature
Edward J. O'Reilly & Alexandra Olaya-Castro
Nature Communications, 9 January 2014, 5, Article number:3012 | doi:10.1038/ncomms4012

Abstract: Advancing the debate on quantum effects in light-initiated reactions in biology requires clear identification of non-classical features that these processes can exhibit and utilize. Here we show that in prototype dimers present in a variety of photosynthetic antennae, efficient vibration-assisted energy transfer in the sub-picosecond timescale and at room temperature can manifest and benefit from non-classical fluctuations of collective pigment motions. Non-classicality of initially thermalized vibrations is induced via coherent exciton-vibration interactions and is unambiguously indicated by negativities in the phase-space quasi-probability distribution of the effective collective mode coupled to the electronic dynamics. These quantum effects can be prompted upon incoherent input of excitation. Our results therefore suggest that investigation of the non-classical properties of vibrational motions assisting excitation and charge transport, photoreception and chemical sensing processes could be a touchstone for revealing a role for non-trivial quantum phenomena in biology.

See also:

Cartwright, J. Quantized vibrations are essential to photosynthesis, say physicists, (22 January 2014)

Tyler, D. Explaining the extreme efficiency of photosynthesis. ARN Literature Blog (16 April 2007)

Tyler, D. The latest thinking on how photosynthesis evolved. ARN Literature Blog (11 February 2007)

Categories: Anti-Science News

Darwin Day approaches

It's time to dust off your Darwin costume again: less than a month remains before Darwin Day 2014!

Categories: Pro-Science News

Continued progress in South Carolina?

At its January 8, 2014, meeting, the South Carolina state board of education voted to adopt a new set of science standards, rejecting two different proposals that would have compromised the treatment of evolution in the process.

Categories: Pro-Science News

Human Brain Development as a Symphony

ID the Future - Fri, 2014-01-10 12:35
Listen Now. On this episode of ID the Future, hear about a recent study from scientists at Yale that found that "human brain development is a symphony in three movements." The human brain develops through distinct patterns in gene...
Categories: Anti-Science News

Thinking of Jeff Jacoby and His Son Caleb

Jeff, the Boston Globe columnist, has long been a friend of the ID movement. David Klinghoffer
Categories: Anti-Science News

The "Other Flagellum" Is Also a Design Wonder

The kind of flagellum that makes sperm swim looks simpler than the bacterial rotary motor. Yes, it looks that way. Evolution News & Views
Categories: Anti-Science News

Eugenic Sundays

Before there was Evolution Sunday, there were eugenic Sundays, preached, more or less, from the same pulpits. Michael Egnor
Categories: Anti-Science News

In Virginia, an Academic Freedom Bill Attracts Ire

Why the fuss? Joshua Youngkin
Categories: Anti-Science News

Just Too Simple! Needs More Math

In an article for Human Events last month, I wrote a very simple introduction to intelligent design. Granville Sewell
Categories: Anti-Science News

Is Robert Richards Right to Deny that Hitler Was a Darwinian?

Richards claims that I played a "sly trick" by translating "Entwicklung" as "evolution" in some passages in Mein Kampf. Richard Weikart
Categories: Anti-Science News

Yale Finds Choreography in the Brain

Symphonies and ballets, generally speaking, are intelligently designed. How about the one in your skull? Evolution News & Views
Categories: Anti-Science News
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