Tuesday, September 11, 2012

Red life forms on Mars - Halophiles?

Opportunity on Meridiani Planum Mars  NASA

BBC Science correspondent Rachel Buchanan wrote an article about a research project in pink life led by Dr Bonnie Baxter in which Dr Shil DasSharma has participated:
The Great Salt Lake in Utah has an otherworldly quality to it. It is a pink-tinged hyper-saline lake trimmed with a halo of salt that encrusts everything it touches.

This inland sea is home to dozens of species of salt-loving micro-organisms - so called halophiles - that thrive in the sodium-chloride-rich soup.

The lake and surrounding Bonneville Salt Flats are the remnants of a much larger, ancient body of water - Lake Bonneville - which drained away thousands of years ago.

But despite the lake's historic existence, little is known about its curious inhabitants, and that is something Dr Bonnie Baxter, of Salt Lake City's Westminster College, plans to change.

She has teamed up with leading halophile experts, including Dr Shil DasSarma of the University of Maryland, to take the first inventory of the lake's microbes.
Dr Baxter has similar aspirations for her Salt Lake inhabitants.

They employ solar-powered salt pumps to keep their internal salt concentrations lower than the water around them. But to drive those pumps, the microbes need to be at the surface which means basking in the Sun's damaging ultraviolet light all day.

But therein lies their powerful secret. The pink colour of the lake is due, in part, to the pigments - carotenoids - that the lake's microbes produce.

These shield their DNA from damage, like an in-built sunscreen, a characteristic Dr Baxter believes could be exploited.

Bonneville Salt Plains Utah

In Dr DasSarma, she has a partner of impeccable pedigree for the project. He was the first to sequence the genome of a halophile - Halobacterium species NRC-1 - in 2000.

Work on its Utah cousins has only just begun but Dr DasSarma says their initial results are showing just how novel these organisms are.

When you compare the DNA of a new species to a gene bank to see if their genes resemble those of known organisms, "normally, three out of four times you find something similar," Dr DasSarma said.

"But when you do this with the Salt Lake, the majority of genes are novel - they are like nothing on Earth."

It is appropriate then that parallels are being drawn between locations like this and Meridiani Planum on Mars. This is where Nasa's Opportunity rover has discovered it is parked on top of an evaporate basin like Utah's Bonneville flats, the remnants of an ancient Martian salty sea.

As the conditions on early Mars got colder and harsher, it lost liquid water through evaporation or sequestration into permafrost.

Remaining bodies of water would have been increasingly salty places, and then finally all liquid water disappeared, and the salt deposits eventually lithified into the evaporate rocks the rover sees today.

Any early Martian microbe would have had to withstand a high salt environment and intense UV radiation. Sound familiar?

Rachael Buchanan
Read the entire article in BBC NEWS Science/Nature May 18 2004

Monday, September 10, 2012

Shil DasSarma - first life pink?

Professor Shil DasSarma University of Maryland marinebiogech.org

Ker Than writes about a suggestion by microbial genetist Shiladitya DasSarma from University of Maryland Center of Marine Biotechnology, that early life on Earth may not have been green nor black but rather pink!
The earliest life on Earth might have been just as purple as it is green today, a scientist claims.

Ancient microbes might have used a molecule other than chlorophyll to harness the Sun's rays, one that gave the organisms a violet hue.

Chlorophyll, the main photosynthetic pigment of plants, absorbs mainly blue and red wavelengths from the Sun and reflects green ones, and it is this reflected light that gives plants their leafy color. This fact puzzles some biologists because the sun transmits most of its energy in the green part of the visible spectrum.

"Chlorophyll was forced to make use of the blue and red light, since all the green light was absorbed by the purple membrane-containing organisms," said William Sparks, an astronomer at the Space Telescope Science Institute (STScI) in Maryland, who helped DasSarma develop his idea.
LiveScience 2007

As a beginner student of the subject, IMHO discussion of the pigment colours on early life forms upon Earth is a good sample of using natural selection as the main tool for explaining the evolution of life.

The idea is there and is fitted to the theoretical discussion of how green might have become the dominant colour and chlorophyll take the leading position in plant life.

Let us suppose a fight for survival on early Earth - let us assume that we need sun to generate energy - who might be competing forcing the choice between black, pink, blue and green?

Indeed, a good show case of evolutionary biology at work explaining the greenness of the plant world!

Friday, September 7, 2012

Pea aphid photosynthesis!

Pea aphid (greenflie) sucking sap

This is a God and Molecular Biology bookmark
Will we ever... photosynthesise like plants
Ed Yong
BBC News Future Science and Environment September 8 2012
As a rule, animals cannot photosynthesise, but all rules have exceptions. The latest potential deviant is the pea aphid, a foe to farmers and a friend to geneticists.

Last month, Alain Robichon at the Sophia Agrobiotech Institute in France reported that the aphids use pigments called carotenoids to harvest the sun’s energy and make ATP, a molecule that acts as a store of chemical energy. (Nature 2010)

The aphids are among the very few animals that can make these pigments for themselves, using genes that they stole from fungi.

Green aphids (with lots of carotenoids) produced more ATP than white aphids (with almost none), and orange aphids (with intermediate levels) made more ATP in sunlight than in darkness.

Thursday, August 30, 2012

Crucially important Chlorophyll f

Stromatolites today
Hamelin Pool Marine Nature Reserve, Australia
Lecture materials in Florida International University FIU

"Chlorophyll f was announced to be present in cyanobacteria and other oxygenic microorganisms that form stromatolites in 2010." (wikipedia)
The point is that chlorophyll f is able to use infra-red light for energy.

Quite a point!

Chemical structure
The only chemical difference between chlorophyll f and a is an additional oxygen atom and two less hydrogen atoms in f.

Chlorophyll f        Chlorophyll a
C55H70O6N4Mg    C55H72O5N4Mg

How can such a small structural difference make such a big functional difference?

Origins of atmosphere!

Cyanobacteria cell

The presence of chlorophyll f in cyanobacteria is of utmost theological significance for Creation.

The earliest currently known signs of life on planet Earth are cyanobacteria found on about 3.5 billion years old basalt in West Australia [myBlog].

Scientists suggest that cyanobacteria began to produce oxygen using photosynthesis and that eventually Earth got the atmosphere from this process. Oxygen rich atmosphere and water make life possible as we know it. Chlorophyll f would be the engine for that - and with infra-red!

Theological significance
If it turns out that this is what actually happened at the beginning of life upon Earth the process is  highly significant when we look at the grander picture of life on our planet. There was no haphazard random beginning of some anomalous organic thing that evolved into this and that. Instead, the beginning of life on Earth in oxygen producing highly sophisticated bacteria with DNA seems ludicrously important and meaningful for the entire Creation.

Don't you agree?

Wednesday, August 29, 2012

Chlorophyll molecule photosystems

Wikipedia encylopedia tells
Chlorophyll molecules are specifically arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts.

In these complexes, chlorophyll serves two primary functions. The function of the vast majority of chlorophyll (up to several hundred molecules per photosystem) is to absorb light and transfer that light energy by resonance energy transfer to a specific chlorophyll pair in the reaction center of the photosystems.

The two currently accepted photosystem units are Photosystem II and Photosystem I, which have their own distinct reaction center chlorophylls, named P680 and P700, respectively. These pigments are named after the wavelength (in nanometers) of their red-peak absorption maximum.

The identity, function and spectral properties of the types of chlorophyll in each photosystem are distinct and determined by each other and the protein structure surrounding them. Once extracted from the protein into a solvent (such as acetone or methanol), these chlorophyll pigments can be separated in a simple paper chromatography experiment and, based on the number of polar groups between chlorophyll a and chlorophyll b, will chemically separate out on the paper.

How does this wonder of nature work?

Discovery of chlorophyll structure

Chlorophyll is among the finest masterpieces of God's creation of natural world and is not exactly a simple thing. It has taken some of the sharpest minds of humanity to try to decipher what it is that makes plants green and how it works in its vital tasks in making life possible on planet Earth. The work of leading scholars has been rewarded with several Nobel prices in recognition of its significance. Chlorophyll research is still going on with full steam today as a hot topic of molecular biology.

Richard Willstätter
Richard Willstätter (1872-1942)
Scientists first began to recognize the molecular structure of chlorophyll at the beginning of the 20th century especially through the work of the German organic chemist Richard Willstätter (1872-1942).

Of Jewish origins from Karlsruhe, Richard Willstätter worked from 1896 in the University of Munich. In 1905 he moved to  ETH Zürich where he solved the structure of chlorophyll a and b.

Willstätter received the 1915 Nobel Price in Chemistry for studies on the structure of plant pigments and especially chlorophyll. (Presentation of the price)

ETH Zürich ranks among the top universities in the world and its researchers have so far received 20 Nobel prices, most recently in 2010.

Willstätter's discovery was the first time that the element Magnesium (atomic weight 12) was found to have a central role in the functioning of living organisms.

Hans Fischer
Hans Fischer (1881-1945)
In 1940 the structure of chlorophyll was described in fuller detail by another German organic chemist Hans Fischer (1881-1945). He won the 1930 Nobel Price in Chemistry for his work on the pigments in blood (bilirubin, haemin), bile, chlorophyll in plant leaves, and the chemistry of the fundamental element in all of them, pyrrole.

Just at the end of Second World War his Munich institute and his life work there were destroyed in Allied bombing. This was too much for Hans Fischer and he committed suicide March 31, 1945. (Germany surrendered unconditionally May 2, 1945).

Robert Burns Woodward
Robert Burns Woodward (1917-1979)
In 1960 American chemist Robert Burns Woodward (1917-1979) published a total synthesis of the chlorophyll a molecule using as research tools both infrared and nuclear magnetic resonance spectroscopy and stereochemistry.

R.B. Woodward is considered among the finest organic chemists of the 20th century. In 1965 he received the Nobel Price in Chemistry for his outstanding work on organic synthesis (ref).

Following Woodward's example, "synthetic chemists have always looked for elegance as well as utility in synthesis" (ref). In doing this they are emulating the Creator of the world who combines functionality and elegance in all His works!

Ian Fleming
Ian Fleming (1935-) Home page
In 1967 an updated full model of chlorophyll a molecule was presented by English organic chemist, University of Cambridgen professor Ian Fleming (1935-) .

Molecular structure of chlorophyll a

3-D model of chlorophyll a molecule
The chemical formula of Chlorophyll a is C55H72O5N4Mg

The heart of chlorophyll a - which is the most common form in Nature - has a single Magnesium ion (green in the model). The core is surrounded by four Natrium (blue) and five Oxygen atoms (red) and framed in 55 Carbon (black) and 77 Hydrogen atoms (white).

The long "antenna" is a phytol chain. "Phytol is an acyclic diterpene alcohol that can be used as a precursor for the manufacture of synthetic forms of vitamin E and vitamin K1. In ruminants, the gut fermentation of ingested plant materials liberates phytol, a constituent of chlorophyll, which is then converted to phytanic acid and stored in fats." (wikipedia)

Chlorophyll a structure

Tuesday, August 28, 2012

Why green leafs instead of black ?

Green chlorophyll and sunlight
Green nature wallpapers

The somewhat surprising question in the title comes from the fact that Nature could utilize sunlight more efficiently if chlorophyll would be black. By rejecting the green wavelength plants get their green colours but loose part of the energy arriving from the Sun .

Word chlorophyll is derived from Greek words χλωρος, chloros ("green") and φύλλον, phyllon ("leaf").

Chlorophyll is crucially important for life on planet Earth as it is in the core of photosynthesis. It is a very complicated molecular structure built on Magnesium atom with its antennae for catching photons. Chlorophyll is used by green plants and also by some important bacteria and algae.

Klorofylli A ja B torjuvat vihreän valon taajuuden
Why green?
According to modern understanding all natural chlorophyll has its origins in the earliest life forms when algae were producing it. But why they reject green light?

Evolutionary Biology is unable to explain why since for the survival of the fittest it would seem more efficient to utilize the entire spectrum leaving chlorophyll black. Shil DasSarma from the University of Maryland suggest that we should not view evolution as a strictly optimized engineering project. As in the case of chlorophyll being green, evolution is not natural engineering that automatically chooses the best fit. Rather, evolving life has to deal with the realities of the environment and accidents of life and is organic rather than mechanical. According to Berman life forms evolve according to the conditions, limitations and possibilities given by reality and not by pure utilitarian logic and natural laws aimed at fitness peak.

Early life on Earth may have been a theatre for bitter fight for survival of the fittest in competition for energy with possibly dominating single cell arkhea that used especially green light through retinal (vitamin A aldehyde) molecule. Perhaps competition from such pink life forms pressured algae to evolve towards chlorophyll processes that reject green light. (Why would energy form a given color in the spectre of sun light be exclusive, though?)
(Read more about DasSarma's views in LiveScience 2007).

Scientific research progresses in this way by questioning also apparently self-evident facts and by suggesting new and challenging theories and hypotheses.  In the evolution of Evolutionary Biology some ideas survive, grow and develop while others wither and die and are thrown in the dust bin of the history of science.

Theological comment
And God said, “Let the water under the sky be gathered to one place, and let dry ground appear.” And it was so. God called the dry ground “land,” and the gathered waters he called “seas.” And God saw that it was good.

Then God said, “Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds. ” And it was so. The land produced vegetation: plants bearing seed according to their kinds and trees bearing fruit with seed in it according to their kinds. And God saw that it was good. And there was evening, and there was morning —the third day.
Genesis 1:9-13 NIV
It would be rather sad if the leafs of the plants were black and grey, wouldn't it?

So let us praise the Lord for the green colour of chlorophyll that together with the majestic Sun create not only oxygen and sugar for all living creatures but also make the Nature so beautiful in the eyes of us people created in His image!

Wednesday, January 4, 2012

Principles of Molecular Biology

What kind of stuff would you study if you decided that after your high school you are going to apply for studies in Biology or Organic Chemistry that also include Molecular Biology and would look at one of the Colleges and Universities in the San Fransisco Bay Area?

Well, if you were accepted as a student and if your teacher happens to be Bob Bruner here is an outline of the kind of materials for your first year of introductory classes that would teach you principles of Molecular Biology:

Bob is also providing frequently updated information to his classes and prospective students in http://bbruner.org/index.htm

All these pages seem to be rich in content and provide a valuable collection of sources from basic stuff to plenty of references to current literature and to Internet  resources.

Materials here are from my course, Principles of Molecular Biology, Fall 2001. I have only slightly updated these materials since that semester; I have tried to keep Internet links and references to basic books in the field current. Much of the information on core molecular biology remains sound, and many of these materials should still be useful to students taking basic molecular biology courses.
Bob Bruner

Please, note that these are purely academic pages and the author has nothing whatsoever to do with my blogs. This is just a reference to one of the many available Web resources and a useful index created by an expert in the field, Bob Bruner, that can be very helpful for those seriously interested in the scientific field of Moleculary Biology.

Tuesday, January 3, 2012

Molecular Biology

Molecular biology is the branch of biology that deals with the molecular basis of biological activity.

This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry.

Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between the different types of DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated.

Writing in Nature in 1961, William Astbury described molecular biology as
not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and [...] is predominantly three-dimensional and structural—which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function.
wikipedia introduction

The following list borrowed from "What is Molecular Biology?" page gives us laymen some idea of the kind of research that is currently going on in the field:

Recent Molecular Biology News

Glorify God

Saint Paul is in no way apologetic when he writes to people living in the centre of classical civilization, Rome.

He is not shamed of Gospel, the message about Jesus Christ he is preaching - and indeed, the message changed Rome, the eternal city, forever and it became what it is today: the centre of Christianity.

He is not shamed of God and says that what can be known about God is manifest for He Himself has shown it to the humans.

What everyone can learn about God, what is so obvious that those who do not worship have nothing to defend themselves?

"For from the creation of the world the invisible things of Him are clearly seen, being understood through the things that are made, even His eternal power and Godhead, so that they are without excuse."
Romans 1:20

Democritus and atomic theory
Democritus (Greek: Δημόκριτος, Dēmokritos, "chosen of the people") (ca. 460 BC – ca. 370 BC) was an Ancient Greek philosopher born in Abdera, Thrace, Greece. He was an influential pre-Socratic philosopher and pupil of Leucippus, who formulated an atomic theory for the cosmos.

Random chance is fundamental principle in the amazing natural philosophy developed by Leucippus and Democritus simply by deep thinking and without any experimentally gained knowledge of the structure of matter. Those undivided things, atoms, run around in some space hitting each other randomly and thus creating lumps that give matter all its properties, such as hardness or softness, colour or taste. 

We might call those "lumps" molecules.

Atom - manifest work of God
Modern nuclear sciences have demonstrated that while Democritus had it right in principle - and this is no small feat for a 4th century BC thinker - there is nothing random in the inner structure of atoms and their nuclei nor in the way molecules are built.

Exact mathematics so bizarre that new ways of thinking with colours had to be developed to deal with it rule the orbits and numbers of electrons around the positive nucleus and the strong and weak and other forces inside the nucleus.

If it can be figured out by thinking it is quite obvious that it may have been made by someone good in mathematics and deep thinking.

Those who deny this have no excuse for not worshipping Him.

Molecular biology
The same obvious wisdom of God is visible in molecular biology.


This is not apologetics or a vain attempt to prove that God exists as shown in the workings of living things on molecular level!

Far from that.

This is just a note in the spirit of Saint Paul that those who deny the divine wisdom in molecular biology have no excuse for not worshipping Him.

No shortcuts to knowledge
Jewish, Christian or Moslem believers in the One God have no shortcut to knowledge because of their faith. Pagan Leupiccus and Democritus showed such an ability of gaining knowledge by thinking that it is almost unparalleled among the humans.

The difference is still important - a believer praises Lord for His works and does not allow anything take His place as some sort of anonymous projection of God into the properties of matter, atoms, molecules and life.

For example, the materialistic atheism of Democritus and his students.

Glorify God!

For when they knew God, they neither glorified Him as God, nor were thankful, but became vain in their imaginations, and their foolish heart was darkened.
Romans 1:21
The purpose of this blog is to do the opposite from the foolish Romans: to glorify God and to be thankful!

As a non-professional I am still curious about life and fascinated by the enormous advances taken in life sciences. This blog is a personal journey to selected subjects and you, the reader, are invited to join me in prayers in this journey to Molecular Biology; feel free to argue for or against the facts and ideas presented here to enrich the discussion on God's wonders!

Sola Dei Gloria!

That which may be known of God is manifest

For I am not ashamed of the Gospel of Christ, for it is the power of God unto salvation to every one who believeth, to the Jew first and also to the Greek. For therein is the righteousness of God revealed from faith to faith; as it is written: "The just shall live by faith."
For the wrath of God is revealed from Heaven against all ungodliness and unrighteousness of men, who hold the truth in unrighteousness, because that which may be known of God is manifest in them, for God hath shown it unto them.
For from the creation of the world the invisible things of Him are clearly seen, being understood through the things that are made, even His eternal power and Godhead, so that they are without excuse.
For when they knew God, they neither glorified Him as God, nor were thankful, but became vain in their imaginations, and their foolish heart was darkened.
Professing themselves to be wise, they became fools, and changed the glory of the incorruptible God into an image made like corruptible man, and to birds and fourfooted beasts and creeping things.
Romans 1:16-23 KJ21