Flowing electrons help ocean microbes gulp methane

Flowing electrons help ocean microbes gulp methane
Electron microscopy (left), and nanoSIMS analyses (right) of slices of individual microbial consortia allowed for unambiguous identification and analysis of thousands of individual cells. nanoSIMS images such as this one give a quantitative picture of the isotopic composition of each cell, and in turn, a measure of each cell's biosynthetic activity in relationship to each cell's neighbors. Credit: Shawn McGlynn/Caltech

Good communication is crucial to any relationship, especially when partners are separated by distance. This also holds true for microbes in the deep sea that need to work together to consume large amounts of methane released from vents on the ocean floor. Recent work at Caltech has shown that these microbial partners can still accomplish this task, even when not in direct contact with one another, by using electrons to share energy over long distances.

This is the first time that direct interspecies electron transport—the movement of electrons from a cell, through the external environment, to another cell type—has been documented in microorganisms in nature.

The results were published in the September 16 issue of the journal Nature.

"Our lab is interested in microbial communities in the environment and, specifically, the symbiosis—or mutually beneficial relationship—between microorganisms that allows them to catalyze reactions they wouldn't be able to do on their own," says Professor of Geobiology Victoria Orphan, who led the recent study. For the last two decades, Orphan's lab has focused on the relationship between a species of bacteria and a species of archaea that live in symbiotic aggregates, or consortia, within deep-sea methane seeps. The organisms work together in syntrophy (which means "feeding together") to consume up to 80 percent of methane emitted from the ocean floor—methane that might otherwise end up contributing to climate change as a greenhouse gas in our atmosphere.

Previously, Orphan and her colleagues contributed to the discovery of this microbial symbiosis, a cooperative partnership between methane-oxidizing archaea called anaerobic methanotrophs (or "methane eaters") and a sulfate-reducing bacterium (organisms that can "breathe" sulfate instead of oxygen) that allows these organisms to consume methane using sulfate from seawater. However, it was unclear how these cells share energy and interact within the symbiosis to perform this task.

Because these microorganisms grow slowly (reproducing only four times per year) and live in close contact with each other,  it has been difficult for researchers to isolate them from the environment to grow them in the lab. So, the Caltech team used a research submersible, called Alvin, to collect samples containing the methane-oxidizing microbial consortia from deep-ocean methane seep sediments and then brought them back to the laboratory for analysis.

Flowing electrons help ocean microbes gulp methane
Pictured is a high magnification image of sediment enriched in syntrophic consortia. In the center of the image is an overview of sediment containing cells, and individual - roughly spherical - microbial communities are shown at high magnification at the ends of lines extending from the center. Fluorescent signals show the ANME-2c archaeal subgroup in red, and sulfate reducing bacteria are shown in green. Sediment particles appear yellow. Credit: Grayson Chadwick/Caltech

The researchers used different fluorescent DNA stains to mark the two types of microbes and view their spatial orientation in consortia. In some consortia, Orphan and her colleagues found the bacterial and archaeal cells were well mixed, while in other consortia, cells of the same type were clustered into separate areas.

Orphan and her team wondered if the variation in the spatial organization of the bacteria and archaea within these consortia influenced their cellular activity and their ability to cooperatively consume methane. To find out, they applied a stable isotope "tracer" to evaluate the metabolic activity. The amount of the isotope taken up by individual archaeal and bacterial cells within their microbial "neighborhoods" in each consortia was then measured with a high-resolution instrument called nanoscale secondary ion mass spectrometry (nanoSIMS) at Caltech. This allowed the researchers to determine how active the archaeal and bacterial partners were relative to their distance to one another.

To their surprise, the researchers found that the spatial arrangement of the cells in consortia had no influence on their activity. "Since this is a syntrophic relationship, we would have thought the cells at the interface—where the bacteria are directly contacting the archaea—would be more active, but we don't really see an obvious trend. What is really notable is that there are cells that are many cell lengths away from their nearest partner that are still active," Orphan says.

To find out how the bacteria and archaea were partnering, co-first authors Grayson Chadwick (BS '11), a graduate student in geobiology at Caltech and a former undergraduate researcher in Orphan's lab, and Shawn McGlynn, a former postdoctoral scholar, employed spatial statistics to look for patterns in cellular activity for multiple consortia with different cell arrangements. They found that populations of syntrophic archaea and bacteria in consortia had similar levels of metabolic activity; when one population had high activity, the associated partner microorganisms were also equally active—consistent with a beneficial symbiosis. However, a close look at the spatial organization of the cells revealed that no particular arrangement of the two types of organisms—whether evenly dispersed or in separate groups—was correlated with a cell's activity.

To determine how these metabolic interactions were taking place even over relatively long distances, postdoctoral scholar and coauthor Chris Kempes, a visitor in computing and mathematical sciences, modeled the predicted relationship between and distance between syntrophic partners that are dependent on the molecular diffusion of a substrate. He found that conventional metabolites—molecules previously predicted to be involved in this syntrophic consumption of methane—such as hydrogen—were inconsistent with the spatial activity patterns observed in the data. However, revised models indicated that electrons could likely make the trip from cell to cell across greater distances.

"Chris came up with a generalized model for the methane-oxidizing syntrophy based on direct , and these model results were a better match to our empirical data," Orphan says. "This pointed to the possibility that these archaea were directly transferring electrons derived from methane to the outside of the cell, and those electrons were being passed to the bacteria directly."

The samples of bacteria and archaea from the ocean floor were collected from the methane seeps at Hydrate Ridge, just 62 miles off the coast of Oregon. Using a three-person submersible called Alvin, the researchers navigated to sites for sampling of background sediment as well as sediment from the bubbling methane seeps. Video shows the vehicle’s robotic arm collecting a push core of methane seep sediment overlaid with an orange microbial mat. Credit: Victoria Orphan and edited by Roland Hatzenpichler/Caltech

Guided by this information, Chadwick and McGlynn looked for independent evidence to support the possibility of direct interspecies electron transfer. Cultured bacteria, such as those from the genus Geobacter, are model organisms for the direct electron transfer process. These bacteria use large proteins, called multi-heme cytochromes, on their outer surface that act as conductive "wires" for the transport of electrons.

Using genome analysis—along with transmission electron microscopy and a stain that reacts with these multi-heme cytochromes—the researchers showed that these conductive proteins were also present on the outer surface of the archaea they were studying. And that finding, Orphan says, can explain why the spatial arrangement of the syntrophic partners does not seem to affect their relationship or activity.

"It's really one of the first examples of direct interspecies electron transfer occurring between uncultured microorganisms in the environment. Our hunch is that this is going to be more common than is currently recognized," she says.

Orphan notes that the information they have learned about this relationship will help to expand how researchers think about interspecies microbial interactions in nature. In addition, the microscale stable isotope approach used in the current study can be used to evaluate interspecies electron transport and other forms of microbial symbiosis occurring in the environment.

These results were published in a paper titled, "Single cell activity reveals direct electron transfer in methanotrophic consortia."


Explore further

Seeing protein synthesis in the field

More information: "Single cell activity reveals direct electron transfer in methanotrophic consortia." Nature (2015) DOI: 10.1038/nature15512

"Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis." Science 20 July 2001: Vol. 293 no. 5529 pp. 484-487 DOI: 10.1126/science.1061338

Journal information: Science , Nature

Citation: Flowing electrons help ocean microbes gulp methane (2015, September 18) retrieved 21 September 2019 from https://phys.org/news/2015-09-electrons-ocean-microbes-gulp-methane.html
This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.
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JVK
Sep 19, 2015
Excerpt: "It's really one of the first examples of direct interspecies electron transfer occurring between uncultured microorganisms in the environment. Our hunch is that this is going to be more common than is currently recognized," she says.

Direct interspecies electron transfer occurring between uncultured microorganisms is likely to be perturbed by viruses that pirate the nutrient-dependent energy required for signaling. That could be considered in the context of an atoms to ecosystems model that links biophysically constrained nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions to cell type differentiation via the chemistry of protein folding, when protein-folding chemistry is not perturbed by viruses.

Unfortunately, until evolutionary theorists and theoretical physicists acknowledge the role that viruses play, serious scientists are not likely to believe in the pseudoscientists ridiculous theories.

Sep 19, 2015
More crap from the creationist crank JVK

JVK
Sep 19, 2015
Is there a reason others, like Vietvet (aka Steven Taylor) do not want this evidence included in an atoms to ecosystems model that links biophysically constrained nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions to cell type differentiation via the chemistry of protein folding, when protein-folding chemistry is not perturbed by viruses?

See the question Steven Taylor (aka Vietvet) asked Greg Bear: Search for "Steven Taylor" at http://www.gregbe...2015.htm

See also: The Darwin Code: Intelligent Design without God http://rna-mediat...eg-bear/

Steven Taylor (aka Vietvet) pretends not to know that this is not a creationist vs theorist issue.

Life on earth must be linked from atoms to ecosystems or it could not exist. Viruses may ensure that it does not. See also: http://thedailysh...reg-bear

Is Steven Taylor (aka Vietvet) a terrorist?

Sep 19, 2015
Creationist, and now conspirationist, crank indeed.

Sep 19, 2015
Speaking of creationists like the Pheromone Troll crank here, I wonder what they do of the new OpenTree effort presented in another article today? It has managed to scour the literature for phylogenetic trees, and despite that most are unaccessible pdf format managed to intergrate 2.3 million species. I checked with TalkOrigins phylogenetic calculator [ http://www.talkor...ierarchy ], and the number of (rooted) trees is 1.5569e+14325459 [!].

If there is still a lot of unresolved or conflicting nodes, especially due to the integration, there is still something like a 1:10^10 000 000 likelihood for creationist isolated species (or 'kinds') against what we observe. I used to think that Theobald's effort to mathematically test the LUCA hypothesis with its 10^2000+ (10^2020) factor against creationist/pheromone magic was the best observed fact we would ever see. Sure, this is the same observation all over again, but a factor 10^10^7+ now.

Sep 19, 2015
Being wrong with a factor 100000... [10 million 0s] ...00000, that - the idea of religious/pheromone magic agencies - must be the most wrongly wrong a wrongly wrong ideology ever produced! At a count of 200 0s a line, and 30 lines per A4, that would be a staple of 2000 A4s, or a paper heap 25 cm tall, to record the creationist fail.

Me, I like reality and what our eyes see so much better.

Sep 19, 2015
rna-mediat...eg-bear/
WARNING!!!!
PHISHING SITE AND PSEUDOSCIENCE SITE
DO NOT CLICK THESE LINKS FROM JVK... they will allow JVK to steal personal data from your computer! THEY ARE PRIVATELY OWNED by jk
reported

Is Steven Taylor (aka Vietvet) a terrorist?
Fear based tactic?
your posts are called conspiracist ideation and they're not only conspiracy theory, but also creationist religion
Considering you promote RELIGION over science this makes sense from you

thank you for validating this study

http://www.ploson...tion=PDF

JVK
Sep 19, 2015
Speaking of creationists like the Pheromone Troll crank here, I wonder what they do of the new OpenTree effort presented in another article today?


Thanks for asking. Speaking for myself, I know young earth creationists have already addressed the "Tree of life" nonsense in the Major Evolutionary Blunders article: "Evolutionary Predictions Fail the Reality Test." http://www.icr.or...ictions/

Excerpt:
Evolutionary developmental biologist Sean Carroll describes the implications of the stunning details:

When the sequence of these homeoboxes were examined in detail, the similarities among species were astounding. Over the 60 amino acids of the homeodomain, some mice and frog proteins were identical to the fly sequences at up to 59 out of 60 positions.


In Dobzhansky's (1973) claim, a nutrient-dependent RNA-mediated single amino acid substitution differentiates cell types. What do the "OpenTree" experts claim?

Sep 20, 2015
Speaking for myself, I know young earth creationists have already addressed the "Tree of life" nonsense
except that creationists don't produce SCIENCE
that is a religion, not anything based upon factual observations nor reality
see also: https://en.wikipe...Arkansas

as proven above:
THERE IS NO SCIENCE IN THE CREATIONIST MOVEMENT

Sep 20, 2015
"The biblical record of primeval earth history in Genesis 1-11 is fully historical and perspicuous, including the creation and Fall of man, the Curse on the Creation and its subjection to the bondage of decay, the promised Redeemer, the worldwide cataclysmic deluge in the days of Noah, the post-diluvian renewal of man's commission to subdue the earth (now augmented by the institution of human government), and the origin of nations and languages at the tower of Babel."
http://www.icr.org/tenets

@JVK

I spent some time at your favorite site, Institute for Creation Research. I don't no whether to laugh or cry. What they consider "science" is worse than a joke. Claiming there is evidence of a world wide flood a few thousands years ago is absolutely delusional.

The only reason for you to share their link is that you share their unscientific beliefs.

YOU ARE A YOUNG EARTH CREATIONIST.

JVK
Sep 20, 2015
http://science.sl...splicing

Excerpt: On August 21st, the research team led by Prof. Yigong Shi from School of Life Sciences, Tsinghua University in China published two side-by-side research articles in Science, reporting the long-sought-after structure of a yeast spliceosome at 3.6 angstrom resolution determined by single particle cryo-electron microscopy (cryo-EM), and the molecular mechanism of pre-messenger RNA splicing. Until now, decades of genetic and biochemical experiments have identified almost all proteins in spliceosome and uncovered some functions. Yet, the structure remained a mystery for a long time. The works, primarily performed by Dr. Chuangye Yan, and Ph.D students Jing Hang and Ruixue Wan under Prof. Yigong Shi's supervision, settled this Holy Grail question and established the structural basis for the related area."

JVK
Sep 20, 2015
you do not have the right to make this insinuation


I have the right to ask why biologically uninformed science idiots think they can continue to claim that serious scientists are simple-minded creationists.

The Chinese NSF funded the work cited above. The USNSF, for comparison, funded this "Tree of Life" nonsense. http://phys.org/n...firstCmt

Pay attention to the difference between funding for science and funding for pseudoscience and watch this video. http://thedailysh...reg-bear

See also: http://www.rice.e...ry2.html

"In the last months of 1996, according to James Kohl (Bruce Willis), a lethal virus will wipe out 5 billion people."

Will evolutionary theorists with their "Tree of Life" save US populations from the threat that is almost assuredly being examined in the context of the Chinese researcher's findings on cell type differentiation?

Sep 20, 2015
JVK the young earth creationist idiot is desperate

Linking to a scifi writer interview.

Linking to a review of a scifi movie. " Science fiction it is, but it's effective precisely because it is chillingly almost possible."

Linking to a young earth creationist site..

Sep 20, 2015
I have the right to ask why...think they can continue to claim that serious scientists are simple-minded creationists
@jk
it's NOT A CLAIM if it is TRUE

you've demonstrated you are NOT a serious scientist, and that can be proven by the following evidence:
-linking articles/youtube/facebook/personal instead of studies

-intentionally false interpretations of science studies as proven by the authors

-your libelous remarks attacking actual scientists who refute your claims (Lenski, Extavour, Whittaker)

-comments like "I know young earth creationists have already addressed the" when there is irrefutable evidence that creationists have NO SCIENCE in their religion

-trying to disguise your PSEUDOSCIENCE by attaching scientific names to personal sites for the prestige (like rna-mediated)

-excessive techno-jargon without clear concise definitions (which you refuse to accept)

-admission to committing felonious acts

FACT - you are a PSEUDOSCIENCE religious poster

JVK
Sep 20, 2015
Linking to a scifi writer interview.


Greg Bear worked/works with the FBI on counter-terrorism because he was already aware of the links from virus-driven pathology to pheromone-controlled reproduction when he published "Blood Music" in 1985, which was shortly before serious scientists published:

"RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon'
http://mcb.asm.or...abstract

See also: http://www.ncbi.n...NBK6360/
"If DNA and DNA replication proteins originated in viruses,7 one can imagine that DNA replication mechanisms have been transferred from viruses to cells (fig. 2). This possibly occurred either at different stages of viral evolution (giving birth to various types of cellular lineages with different DNA replication modes), or only at the symmetric stage. In the latter case, the first DNA cells would have had an immediate advantage..."

JVK
Sep 20, 2015
Does anyone think it is coincidental that Greg Bear's works were linked from the character played by Bruce Willis in 12 Monkeys, named James Kohl, who was assigned to save 5 million people from a viral threat in the year 1996, which was the year after my non-fiction book (co authored by Robert Francoeur) was published?

Can anyone confirm or deny the use of the letters of the Aramaic alphabet as indicators of the 20 amino acids and 2 stop codons that are the building blocks for the creation of all nutrient-dependent biodiversity on this planet?

http://blog.crist...ids-dna/

Is anyone here not a biologically uninformed science idiot or terrorist?

Sep 20, 2015
http://www.cristi...ten.aspx

@JVK

You're a slut when it comes to your choice of sites you think back up your comments.

"New" Vision of the Tarot: the Soul-based Reading
You Are the Colours You Choose
The Colour Rose: Colour is the Mirror of Consciousness
Initiation to Archangel Michael Course
Aura-Soma Level 1 Foundation in Slovenia
Foundation Course in Numerology
The 72 Angels of the Kabbalah
Esoteric Astrology
Aura-Soma®: Colour as Consciousness
Numbers and the Development of Consciousness

You've admitted not being a geologist nor a theologian. You've failed at history and proved you
are not a biologist. YOU are a dumb ass for for your choice of links.


Sep 22, 2015
"Twelve Monkeys" (1995)
http://www.imdb.c...0114746/

Excelent movie. Great performance of Willis and Pitt. Madeleine Stowe did great too, but that wasn't a surprise...

Bruce Willis................as James Cole
Madeleine Stowe.......as Kathryn Railly
Brad Pitt ....................as Jeffrey Goines

JVK
Sep 22, 2015
Bruce Willis................as James Cole

Bruce Willis played James Kohl

See also: https://www.youtu...YAoiCSsI

You've failed at history and proved you are not a biologist.


I'm a medical laboratory scientist who has predicted the future that biologically uninformed idiots are leading us into. But, as Steven Taylor (aka Vietvet) knows, Greg Bear did that best in his novels from 1985, 1999, and 2003.

See: http://www.gregbe...2015.htm
From: Steven Taylor
Location: United States
Date: 01/28/2015

James V. Kohl claims you incorporated his model of nutrient dependent, pheromone ecological adaptation in your Darwin novels. Any truth to that?

See also: https://www.faceb...ediated/ which includes my response to this published work: mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3 http://www.nature...192.html

Sep 22, 2015
"Twelve Monkeys" (1995)

Release Info:
USA 27 December 1995 (premiere)
USA 29 December 1995 (limited)

Production Draft: June 27, 1994
http://www.dailys...eys.html
http://www.amazon...0ABLI15Y

JVK
Sep 22, 2015
What's your point "JustAnotherGuy" Are you claiming that serious scientists are 30 years overdue to understand what a science fiction author knew -- or just 20 years overdue?

BLOOD MUSIC Hardcover – 1985
http://www.amazon...od+music

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon - 1985 http://mcb.asm.or...abstract

JVK
Sep 22, 2015
See also: Linking Viral Discovery with Causality Sep 23 2015 | 9:00 AM PT

https://www.labro...d-sept23

She may be presenting something about cell type differentiation that Greg Bear did not know 30 years ago.

Evolutionary theorists and theoretical physicists are hoping they will not look more foolish after the presentation than they do now.

Sep 23, 2015
What's your point "Just Another Guy"
Just wondering why one of my fav sci-fi movies is being linked to several people and its works with no apparent reason.

Sep 24, 2015
Bruce Willis................as James Cole

Bruce Willis played James Kohl
ROTFLMFAO

Narcissism, Dunning-Kruger, and sociopathic delusions of grandeur strike again!

ROTFLMFAO

MAN!
my stomach hurts from this one!

JVK
Sep 24, 2015
Just wondering why one of my fav sci-fi movies is being linked to several people and its works with no apparent reason.


See "The Darwin Code: Intelligent Design without God" http://rna-mediat...eg-bear/

The reason to link atoms to ecosystems has always been to answer Schrodinger's question "What is Life?" He challenged de Vries definition of "mutation" and placed the anti-entropic energy of the sun first in the context of quantum physics.

Neo-Darwinian theorists still seem to think they can get away with using de Vries definition and attempts to link it from natural selection to the evolution of biodiversity as if nothing known to serious scientists, like Schrodinger, Dobzhansky, and James Kohl (i.e., me, not the character played by Bruce Willis) had changed during the past century -- despite publication of this 1996 review: http://www.hawaii...ion.html

JVK
Sep 24, 2015
...sociopathic delusions of grandeur strike again!


What makes someone who claimed he was raised by wolves for 10 years also make a claim like that?

Sep 24, 2015
Just wondering why one of my fav sci-fi movies is being linked to several people and its works with no apparent reason.

See "The Darwin Code: Intelligent Design without God" http://rna-mediat...eg-bear/

... and James Kohl (i.e., me, not the character played by Bruce Willis)

Now that's better: "me, not the character". Willis played as "Cole" in "Twelve Monkeys". "Kohl" is unrelated.


Sep 24, 2015
Sorry, editing erased this part:

See "The Darwin Code: Intelligent Design without God" http://rna-mediat...eg-bear/

Watch "Twelve Monkeys" once and for all. Also, check the links and learn the movie facts please: "Inspired by LA JETEE, a Chris Marker Film"
http://www.imdb.c...0056119/

JVK
Sep 24, 2015
https://en.wikipe...t%C3%A9e Excerpt: From a philosophical point of view, La Jetee is an existentialist tale of doomed existence, inevitability, and predetermined death.

If you think Chris Marker was the source for the "viruses will kill 5 billion" plot you have an amusing fixation on the philosophy of science fiction, which can be compared to Greg Bear's raw insight that predicted his science fiction would become fact.

See the acknowledgments section of Darwin's Children:

Excerpt: Acknowledgments:

Special thanks to Mark Minie, Ph.D., and Rose James, Ph.D.; Deirdre V. Lovecky, Ph.D.; Dr. Joseph Miller; Dominic Esposito of the National Cancer Institute; Dr. Elizabeth Kutter; Cleone Hawkinson; Alison Stenger, Ph.D.; David and Diane Clark; Howard Bloom and the International Paleopsychology Project; Cynthia Robbins-Roth, Ph.D., James V. Kohl, Oliver Morton, Karen Anderson, Lynn Caporale, and Roger Brent, Ph.D.

"James V. Kohl" is me.

JVK
Sep 24, 2015
For a link from ions/atoms to ecosystems via what is known about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding chemistry that links sunlight and water to the human thirst mechanism and healthy longevity, see:

https://www.faceb.../?type=1

Hopefully, it has become clear to all serious scientists that viruses perturb the thirst mechanism, which is why it can become an issue in the emergency room presentation of patients with black tongues who claim they are not thirsty, but also tend to die of virus-caused dehydration.

JVK
Sep 24, 2015
Narcissism, Dunning-Kruger, and sociopathic delusions of grandeur strike again!


"A man's got to know his own limitations." Clearly, Captain Stumpy's limitations are among the most severe when it comes to expressing any intelligent thoughts whatsoever at any time.


Sep 25, 2015
...Excerpt: From a philosophical point of view, La Jetee is an existentialist tale of doomed existence, inevitability, and predetermined death.

At last! a related link! Thanks: https://en.wikipe...t%C3%A9e

That sentence is from the "Interpretation" section of "La Jetée" article. Shows analyses and meanings of that movie. To relate it with "Twelve Monkeys" read: https://en.wikipe..._Monkeys
Besides that the plot descriptions shows the countless coincidences, both articles links the movies directly.

If you think Chris Marker was the source for the "viruses will kill 5 billion"

Don't think, read the plot. Chris Marker's "La Jetée" is about the "World War III", not viruses. The viruses's plot is not from him, nor from director Terry Gilliam, nor from Greg Bear, not from anyone but David and Janet Peoples who wrote it in 1994. I told you already: http://www.dailys...eys.html

Sep 25, 2015
See the acknowledgments section of Darwin's Children:
Special thanks to.....
"James V. Kohl" is me.

Now, that is how you can properly relate your name to something. Congratulations. Neither Greg Bear, nor you, are credited in "Twelve Monkeys": http://www.imdb.c...tt_cl_sm

Thanks. "Case closed".

I suppose this trash was all you known about that movie: http://www.rice.e...ry2.html
Here is a good review from that time: http://www.deep-f...emo.html

But better if you watch the movie, "Doc".

Sep 25, 2015
Oh... don't mind about calling you "Doc". Look at this as a compliment.
Check your name, credited in the list from Greg Bear's book, again. Looks like he forgot your title there... why, "Doc"?

Also, I found the "Acknowledgments" section on-line, and a bit more:
"James V. Kohl's The Scent of Eros (1995) is a rich sources of information on pheromones, human communication through smell, and the influence of scent on sexuality"

I suppose most of the scientific information used in "Darwin's Children" (2003) was obtained from the proper specialists about viruses, biology, etc, etc. included in that list.

You sell scents.. right? "Doc"?

Sep 25, 2015
@JustAnotherGuy
he hasn't seen the movie

.

If you think Chris Marker was the source for the "viruses will kill 5 billion" plot...
@jk
yeah, because who the heck has ever heard of "The Stand", the 1918 flu epidemic or the black death from 1346–53 to draw inspiration from, right?

& it's not like anyone ever thought to use biological warfare for genocide before WW1 either, right? [sarcasm, hyperbole and satire]
Captain Stumpy's limitations are among the most severe when it comes to expressing any intelligent thoughts
HYPERBOLE, right, mr pot?

LMFAO

by all means: tell us about your decades experience in diagnostic medicine again? is that the reason you refuse to answer questions with specifics? is that why you can't actually support your claims with actual science and continually link to religion?

WHY HAVEN'T you answered a single question asked? is it because you don't know, or you are still thumbing thru the bible or creationist literature?

JVK
Sep 28, 2015
I've answered all the pertinent questions about biologically-based cause and effect in a series of published works. Others are rapidly moving forward. See:

https://www.labro...nd-oct28

Abstract

DATE: October 28th, 2015
TIME: 11am Pacific time, 2pm Eastern time

Excerpt: "... the development and health of an individual is influenced by past experiences of that individual's parents.

Research shows, that enriching environments offer opportunities for improved sensory, motor, cognitive, and social stimulation. This improved stimulation has a multitude of positive effects, from increasing learning and memory, to reducing the possibility of acquiring depression or many brain disorders including Huntington's diseases, Alzheimer's and stroke. In this webinar we will talk about how current investigation in Epigenetics can affect patient treatment and impacts research in general.

Sep 29, 2015
I've answered all the pertinent questions about biologically-based cause and effect
Except for:
http://www.socioa...ew/24367

and
http://rspb.royal...full.pdf

that means, by definition, any and all other publications are based upon work that is NOT proven, skeptical and highly subjective, thus it can be considered pseudoscience

then there is the complete disregard you give to modern experimental evidence like:
Lenski
Extavour
Whittaker
and so many more

creationist religion is NOT science: proven here
https://en.wikipe...Arkansas


JVK
Sep 29, 2015
Please stop reasserting the same nonsense. People deserve much better explanations of cell type differentiation than pseudoscientists have provided.

Evolutionary theory is past its past-due date and all serious scientists know that.

JVK
Sep 29, 2015
See also http://phys.org/n...ogy.html

The code
is counterintuitive to natural selection.


In less than a month, all neo-Darwinian pseudoscientific nonsense has been eliminated from consideration by serious scientists.

See: Mechanisms of stress in the brain http://dx.doi.org.../nn.4086

See also: Molecular insights into transgenerational non-genetic inheritance of acquired behaviours
http://www.nature...eReviews

Excerpt: Possible mechanisms... during development and adulthood are considered along with...the involvement of epigenetic modifications and non-coding RNAs in male germ cells.

The detailed molecular mechanisms of transgenerational epigenetic inheritance in McEwen et al., can be compared to the possible mechanisms in Bohacek & Mansuy.

JVK
Sep 29, 2015
then there is the complete disregard you give to modern experimental evidence like:
Lenski
Extavour
Whittaker
and so many more


Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways. http://elifescien...kI6.dpuf

Conclusion: Previous work has proposed that different wrapping modes may be used selectively in different DNA metabolic processes (e.g., replication vs recombination) (Sancar et al., 1981; Lohman et al., 1988). How and which of these modes are used for particular processes remains unclear, as experimental proof of this proposition has proven difficult to obtain in vitro. We anticipate that the control of SSB wrapping mode by applied force may be a useful experimental tool to test this hypothesis."

Note: No serious scientist is trying to link mutations to evolution.

Sep 30, 2015
Please stop reasserting the same nonsense
you mean like you never reassert the same thing?
difference between the two of us: my assertions are PROVEN & VALIDATED by experimentation and empirical evidence
...whereas your "ASSertions" are simply hot air and religion
Evolutionary theory is past its past-due date
and this will happen ONLY if you can demonstrate a better theory, like GR/SR replaced Newtonian physics (also note, we still use Newtonian Physics)
No serious scientist is trying to link mutations to evolution
you mean, except for EVERY BIOLOGIST out there, right?
Lenski, Extavour, etc? (PROVEN with validated experiments)

too bad you cant comprehend basic english, eh?

this is the problem with you religious fanatics: you can't see the science!

reality is there regardless of your beliefs

http://www.ploson...tion=PDF

another epic JK FAILURE

Sep 30, 2015
Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways. http://elifescien...kI6.dpuf
@jk
you have NO IDEA WTF the study is talking about, do you?

by all means, feel free to be very specific and tell us what you THINK this link/study is saying, because it is not dealing with what you THINK it is ...

it also doesn't support your quote "No serious scientist is trying to link mutations to evolution"

while you are at it... why don't you specifically tell everyone what YOU THINK the following means? "pN"

Why do you continue to post links when you have NO IDEA what they discuss or demonstrate, and then claim they mean something they don't?
(rhetorical)

JVK
Sep 30, 2015
Metabolic theory predicts whole-ecosystem properties http://www.pnas.o...abstract

"A theory is presented which shows how the metabolism of individual organisms controls the flow of carbon through ecosystems. The theory synthesizes top-down, ecosystem-level and bottom-up, organism-level approaches to ecological energetics and material cycles. The theory predicts a very simple straight-line relationship between residence time of carbon molecules and the ratio of whole-ecosystem biomass to primary productivity. This and additional predictions for total throughfow and recycling are supported by numerical models and data from real ecosystems. The theory provides a powerful way to understand the roles of organisms in ecosystem processes at scales from local habitats to the biosphere. Such an understanding is important for addressing the impacts of human-caused changes in climate, land use, and biodiversity."

JVK
Sep 30, 2015
Re: Metabolic theory predicts whole-ecosystem properties

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche...

Oct 01, 2015
Metabolic theory predicts...
See also: Nutrient-dependent pheromone-controlled
IOW - no, you don't know what the study means

RIGHT. thanks for demonstrating that

also note: your "model" is debunked
you can read more about that here: http://www.socioa...ew/24367

Jones is both educated and well versed in actual biological processes and doesn't attempt to use the "appeal to authority", instead debunking you with actual known and validated science and biological processes

and another thing: there is NO SCIENCE in your religion (creationist)
https://en.wikipe...Arkansas

JVK
Oct 01, 2015
Jones is both educated and well versed in actual biological processes and doesn't attempt to use the "appeal to authority"


Andrew Jones is a biologically uninformed fool who cited PZ Myers blog posts for comparison to my series of published works based on the scientific authority of Bruce McEwen, Robert L. Moss, and many others.

See: Mechanisms of stress in the brain http://www.nature...086.html

In my 2013 review, I wrote: "Nature: The genetically predisposed embryonic migration of GnRH neurons to the hypothalamus is controlled by in utero nutrient stress and social stress (see Fig. 1). Stress alters fine-tuning, which is required for the homeostasis that supports the optimal epistatic outcome of gestation.

Nurture: Genetic predispositions, nutrient stress, and social stress continue to impact prenatal and postnatal development of the brain during sexual differentiation (Makris et al., 2013)."

Oct 02, 2015
Andrew Jones is a biologically uninformed fool
but you've said this about Lenski, Dr. Extavour, Dr. Whittaker, and just about every other actual scientist who refuted your claims and debunked your childish outbursts of religious propaganda in the past as well... so he is in good company, unlike you: who are you trying to imitate? the Spanish Inquisition?
https://www.youtu...XHY2OXGE

you seem to hate anyone who has an education: is that because your past when you failed out of college?
is that why you lie about being a diagnostician?
and claim mensa membership?

so, to reiterate
IOW - no, you don't know what the study means

RIGHT. thanks for demonstrating that
thanks for the demonstration of misrepresentation, misdirection, red herring and strawman arguments

Oct 02, 2015
"Few people are as adamant or ignorant. His excuse is lost faith due to war-time trauma, which also sometimes reinforces the beliefs of others in creationist science linked to God. Even when others do not understand creationist science they realize that it attests to the fact that viruses perturb protein folding and that can thus be linked to all pathology in all individuals of all living genera."
JVK on Oct. 2 2015
http://medicalxpr...ons.html

JVK
Oct 02, 2015
An atoms to ecosystems model links ecological variation to ecological adaptations via what is currently known to serious scientists about nutrient-dependent RNA-mediated gene duplication and how RNA-mediated amino acid substitutions stabilize the organized genomes of all living genera.

No matter how many people put what is known about molecular epigenetics into the context of mutations and evolution their theories will continue to lack explanatory power as others link nutrient-energy to cell type differentiation and link the nutrient-dependent energy that is pirated by viruses to mutations and pathology.

See: Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida
Re: (COI) from more than 400,000 animal species
Excerpt: " COI sequence data can provide an overview of patterns of amino acid evolution across both other groups of arthropods and animal life at large." -- except for the fact that amino acids don't evolve.

JVK
Oct 02, 2015
Re:
...every other actual scientist who refuted your claims and debunked your childish outbursts...


Everyone had the opportunity to offer a model of biologically-based cause and effect for comparison to mine. In the past two years, no one has done that.

"Mutation-Driven Evolution" http://www.amazon...99661731 and Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...24693353 were published on the same day.

Only the refutations of "Mutation-Driven Evolution" have been accepted by serious scientists.

See for example: Competing mice reveal genetic defects http://medicalxpr...tml#nRlv What kind of biologically uninformed science idiot think it is acceptable to ignore the effects of stress-altered protein folding, but proceed to link constraint-breaking mutations to all biodiversity? That was a rhetorical question. Masatoshi Nei did it!

Oct 02, 2015
An atoms to ecosystems model
there is NO SUCH MODEL that is also peer reviewed, validated or even supported by the scientific method, mostly because of the issues between macro physics and quantum physics
reported for PSEUDOSCIENCE

No matter how many people put what is known about molecular epigenetics into the context of mutations and evolution their theories will continue to lack explanatory power
this is directly refuted with the Theory of Evolution
see also: https://en.wikipe...d_theory

Everyone had the opportunity to offer a model of biologically-based cause and effect for comparison to mine. In the past two years, no one has done that
that is because your model does not, in ANY way, undermine or even supplant the Theory of Evolution
See link above

there is no reason to offer evidence to a religious fanatic who will simply ignore it anyway... just like you've done with EVERY scientific link to date

Oct 02, 2015
@jk cont'd
Everyone had the opportunity to offer a model of biologically-based cause and effect for comparison to mine. In the past two years, no one has done that
another reason no one offered another model is simply because your own model is:
1- very confused and while you denigrate mutations, your model actually requires them
2- your model also is already included in the Theory of Evolution because it covers adaptation, which is a part of evolution
3- and most importantly, YOUR MODEL is not a model that can replace what is already known because it ignores what is already known - this is most evident in your ignorance and failure WRT the terms and lexicon of biologists/medical professionals (such as: the word mutation)

until you can actually present biological evidence, i will continue to report all your pseudoscience claims, like your posts above

JVK
Oct 02, 2015
1- very confused and while you denigrate mutations, your model actually requires them


McEwen et al (2015) is supportive of my model. They do not mention mutation or evolution.

Mechanisms of stress in the brain http://www.nature...086.html

"...meeting the demands imposed by stressful experiences through various coping resources can lead to growth, adaptation and learning to promote resilience and improved mental health128,132."

Ecological adaptation via amino acid substitutions links them to the mental health my antagonists do not demonstrate. In most cases, improvement would require a slight difference in diet during a critical period of adaptation that linked a life history transition to one amino acid substitution as exemplified in Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults http://link.sprin...4-0895-5

JVK
Oct 02, 2015
2- your model also is already included in the Theory of Evolution because it covers adaptation, which is a part of evolution


What part does the definition of mutation play in adaptation?


Oct 02, 2015


McEwen et al (2015) is supportive of my model. They do not mention mutation or evolution.

Mechanisms of stress in the brain http://www.nature...086.html


Another delusional reading comprehension fail by JVK.

JVK
Oct 02, 2015
Abstract excerpt: "A key result of stress is structural remodeling of neural architecture, which may be a sign of successful adaptation, whereas persistence of these changes when stress ends indicates failed resilience. Excitatory amino acids and glucocorticoids have key roles in these processes, along with a growing list of extra- and intracellular mediators that includes endocannabinoids and brain-derived neurotrophic factor (BDNF). The result is a continually changing pattern of gene expression mediated by epigenetic mechanisms involving histone modifications and CpG methylation and hydroxymethylation as well as by the activity of retrotransposons that may alter genomic stability."

Nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions link cell type differentiation to genomic stability in all individuals of all species via the physiology of reproduction, not by mutations and evolution.

JVK
Oct 02, 2015
See also: The sea slug that eats the sun https://www.youtu...diXYpY30

See also: Sensory feedback shapes individuality to provide equal space for behavioral excellence http://phys.org/n...ace.html

http://www.pnas.o...39/12110 Excerpt: Chemical cues regulate key ecological interactions in marine and terrestrial ecosystems.

http://www.ncbi.n...3960065/ Excerpt: "THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction..."

JVK
Oct 03, 2015
Fields, Forces, and Flows in Biological Systems (BE.430J)
http://ocw.mit.ed...ll-2004/

"This course covers the following topics: conduction, diffusion, convection in electrolytes; fields in heterogeneous media; electrical double layers; Maxwell stress tensor and electrical forces in physiological systems; and fluid and solid continua: equations of motion useful for porous, hydrated biological tissues. Case studies considered include membrane transport; electrode interfaces; electrical, mechanical, and chemical transduction in tissues; electrophoretic and electroosmotic flows; diffusion/reaction; and ECG. The course also examines electromechanical and physicochemical interactions in biomaterials and cells; orthopaedic, cardiovascular, and other clinical examples."

Re: hydrated biological tissues. Which of these arose via mutation and evolution?

Oct 03, 2015
McEwen et al (2015) is supportive of my model
personal conjecture without evidence
please also note that you are NOT REFERENCED ONCE in said link provided, therefore it does NOT support your "claim" of being "supportive of your model"

just because you believe it doesn't make it true... you've also stated "Creationists are among the serious scientists", which is proven to be not only false, but blatantly so, as the movement has NO SCIENCE in it, proven here: https://en.wikipe...Arkansas

and repeating a lie doesn't make it any more true
Which of these arose
not only is this a an irrelevant red herring, but you also cannot answer with any evidence of your own

argument from ignorance and lack of knowledge doesn't make you correct

it is also the argument called: god of the gaps
see also - https://www.youtu...kg4hMRjs

another epic failure for jk and religion

Oct 03, 2015
http://www.ncbi.n...3960065/ Excerpt: "THIS MODEL DETAILS HOW CHEMICAL ECOLOGY
a far better reference would be the critique of said link found here: http://www.ncbi.n...4049134/

this is also found on the pub med site link you used... also note
Despite his valid publications involving endocrinology, sexuality, and epigenetically induced intraspecies differentiation in model organisms, James V. Kohl overextends his expertise in trying to overthrow established evolutionary theory...
Kohl posits that evolution is exclusively driven by genetically predisposed, nutrient-dependent, and pheromone-controlled behavior and sexual selection. On the molecular level, he references only epigenetic processes (although he does not describe them in detail)
that is enough to completely undermine the entire paper as well as demonstrate your religious fanaticism and failure with reading and comprehension

YOUR MODEL/PAPER is REFUTED

Oct 03, 2015
What part does the definition of mutation play in adaptation?
perhaps you should first familiarize yourself with the definition of mutation: https://en.wikipe...Mutation

you already admit your own model requires them, in your own words (need i re-post that conversation?)

then you should also familiarize yourself with the definition of the term ADAPTATION
https://en.wikipe...aptation

then i suggest further reading here: https://en.wikipe...aptation#Types_of_adaptations

http://www.eoeart.../159530/

all of which answer your question with not only definitions, but actual physical evidence in the form of references and science

if you feel this is not adequate, i suggest either:
proving it with the scientific method and evidence
OR
getting an education and finding out what you are missing because of your fanatical religious beliefs

your choice

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