Archive for the ‘Origin of Life’ Category
To Change the Species – Just Change the Genome!!
The news appeared in most of the leading newspapers that scientists have successfully transplanted the entire genome of one species of bacteria to another. This is carried out by the institute lead by J. Craig Ventor, a prominent participant in the human genome sequencing.
The researchers worked with Mycoplasma mycoides (a microbe that infects goats) because it has one of the smallest genetic blueprints of any known self-replicating organism and lacks cell walls, making it easier to insert new DNA. They isolated its entire genetic code – one chromosome that forms a circle-stripping it of all its proteins, and then added genes to make a host organism blue (to make it easy to pick out in a Petri dish) as well as resistant to the antibiotic tetracycline. The scientists added close relative Mycoplasma capricolum (another goat pathogen) to a solution containing M. mycoides’ genetic material and gently mixed it for a minute. After three hours of incubation, the resulting microbes were exposed to the antibiotic tetracycline.
The Evolution and Natural Selection are played once more in the labs as the variants having favorable mutations (artificially imposed) survived and the rest perished. After three days, large colonies of blue, antibiotic-resistant microbes had formed. Roughly one in 150,000 of the M. capricolum microbes had absorbed the new DNA and transferred it to daughter cells. The daughter cells displayed no trace of their original DNA while taking on the entire form and function of the original bacterium.
The ultimate goal is to make cells that might take carbon dioxide out of the atmosphere and produce methane, used as a feedstock for other fuels. Such an achievement might reduce dependency on fossil fuels and strike a blow at global warming.
Scientists remain unable to create synthetic life in the lab. “If we’re trying to understand the origins of life and cellular life, it would be ideal to have all the chemical components in a soup to spontaneously go together and form a cell”, Venter says, “We’re a long way from that.”
The Bengali Resources at Mukto Mona
While I write on Richard Dawkins and Evolution in my blog, a group named mukto-mona have taken up their pens to write up in Bengali. It’s great to see people scribing for Atheism and Dawkins in Bengali. Let me refer you all to some of the best resources available in Bengali.
1) The first chapter of The God Delusion.
2) A book on Evolution by Bonnya Ahmed – continued for multiple chapters. It is also available as a book at Bangladesh Ekushe Boimela.
3) A Richard Dawkins article on Religion and Evolution.
4) The Journey of Science to find Life – An excellent write up on modern science (especially focussing on the roots of Universe and what is Life) starting from Big Bang to Extraterrestrial life, divided into multiple parts.
The life of Charles Darwin is described in Bengali.
And of course, anybody want to publish their views in Bengali, can send it to them or join a yahoo group called mukto-mona. There are numerous good articles both in English and Bengali published at the site. I bet that anybody will enjoy most of them. To a Bengali living in West Bengal, I would recommend these article since they should know how close they are to someone living accross the border – in Bangladesh.
The Evolution FAQ
I was planning to write about Evolution FAQ for long. It’s boring to fight against all apostates of Evolution visiting their own blogs. Rather, if I can prepare a platform at my own blog to fight those, I get a better opportunity pounce on them. By the way, let me first acknowledge that this particular piece is going to be mostly be compiled from various sources in Internet.
The evolution is best described as :
1. is a fact,
2. is also a number of theories,
3. is Science,
4. is also scientific,
5. is naturalistic and purely mechanistic,
6. is falsifiable,
7. is testable,
8. is predictive,
9. has been observed;
9a. in the field
9b. in the laboratory,
10. has occurred in the past,
11. is still occurring,
12. will continue to occur in the future.
Further, we can also note that evolution:
13. is not atheistic (nor Communistic, Marxist, Leninist, Stalinist, etc.),
14. is not evil,
15. is not mandated by law to be taught in US public schools,
16. is not a cosmological theory (i.e., “it don’t do origins”),
17. is not a religion nor Religion,
18. is not determined by popular opinion (as can be said of any science),
19. is not a socio-political program or paradigm,
20. is not dependent on the supernatural,
21. does not claim that “Man came from apes”,
22. is not progress,
23. has not, will not and cannot be proven (as can be said of any science),
24. Is not random nor relies on ‘blind chance’,
25. does not violate the second law of thermodynamics,
26. Does not deny (a) God(s), and finally,
27. Falsifying evolution does not prove Creation.
Sounds interesting? Continue reading … By the way, my pick of the quote would be :
The honest scientist, like the philosopher, will tell you that nothing whatever can be or has been proved with fully 100% certainty, not even that you or I exist, nor anyone except himself, since he might be dreaming the whole thing. Th us there is no sharp line between speculation, hypothesis, theory, principle, and fact, but only a difference along a sliding scale, in the degree of probability of the idea. When we say a thing is a fact, then, we only mean that its probability is an extremely high one: so high that we are not bothered by doubt about it and are ready to act accordingly. The probability that evolution is the correct explanation of life as we know it may approach 99.9999…9% but it will never be 100%.
However I would like to pick up a few more so called technical questions to answer. The pick of the questions are :
1) What is the application of Evolution, or, in other words, can evolution predict anything?
A very good application can be the creation of hybrid species. These species are been created matching the environment they are going to live, so that they can maximize production. This is derived from the fact that nature does select. If everything were created, we would not be able to create new species.
Many predictions made by theory of evolution are proven true. Darwin predicted the existence of ‘unit of heredity’ that was proved to be gene. And, the genetic similarities the species share among them, are the living evidences of evolution. More recently, the same theory explains the existence of antibiotic-resistant bacteria, who’ve mutated to resist antibiotic (e.g. penicilin), and ‘selected’ to become the majority and can resume attacks.
2) If humans are from monkeys then how does monkeys still exist?
Human beings did not evolve from monkeys. They share a common ancestor with monkeys. And a new species generally comes out of the other only if they are geographically isolated. So one can safely assume, that there were at least two groups of apes/hominoids, one evolved to become humans, the other became monkeys.
3) Even if we accept natural selection, what’s the proof that it leads to speciation?
I should refer to the speciation events observed in the past in front of modern human eyes.
That’s it from my side. I know I could have written a lot more than this, but somehow, I’m satisfied with this. If anybody else suggests me about any common misconception, I am ready to clarify him.
Further reference :
1) FAQ 1 A good technical one.
2) FAQ 2 brief but to the point.
Videos on Evolution
The Discovery channel on Evolution of life on Earth is amazing and entertaining. Here’s the list of of the links -
part 1, part 2, part 3, part 4, part 5, part 6, part 7, part 8, part 9, part 10, part 11, part 12. The program is named as “Walking With Monsters”. The Dinosaurs stared later with the program Walking with Dinosaurs (New Blood) – part 1, part 2 and part 3. The series ends with three parts of Walking with Dynosaurs (The End of Dynasty) – part 1, part 2 and part 3. In fact the entire set uploaded by TruthTheory should be watched.
An knowledgable description of the process is found in Dawkins’ video -
The evolution of the eye. The full video is available in part 1 and part 2, titled The Blind watchmaker. Another video, comparatively less attractive, was the Nice guys finish first.
The wonderful story of Human evolution is at 5 parts -
part 1, part 2, part 3, part 4 and part 5. The series is named as “Human Life – Evolution To Self-Evolution”. It also lists the proofs gathered with respect to human evolution.
Memetics and Cultural Evolution: The Roots of Religion
What is Memetics?
The term “meme” coined and popularized by the biologist Richard Dawkins in his book The Selfish Gene, refers to a “unit of cultural information” (cognitive or behavioral pattern) which can propagate from one mind to another in a manner analogous to genes (i.e., the units of genetic information). Some contemporary examples of meme can be popular proverbs (“Hard work pays”), gossips, health consciousness (“wash hands before eating”), nursery rhymes (even epics and religious books), conspiracy theories, terms and phrases (“Whassup”) and a lot more.
Memeplexe or Meme-complex is a group of Memes; those are interdependent and survive as a ‘colony’ of memes – such as religion, culture or political doctrines.
Memetics, coined as a similar sounding word of Genetics, is an approach to evolutionary models of information transfer based on the concept of the meme. The popular Memetics hypotheses that memes do not replicate only, but refined, recombined or modified in new memes.
Propagation of Memes
The better a meme can be copied; more it will become common part of the culture. This depends on copying fidelity (accuracy of copy), fecundity (rate of copying) and longevity of the meme. The successful propagation of memes depends on various things – experience of the individual, speculation of the individual, social censorship, distinction of source of the meme. Two communities, those who mix rarely, can be thought of as memetically isolated communities, e.g. Americans and Arabs.
Children as the media of meme propagation
As per behavioral evolution, children who are more obedient to their parents get natural selective advantage over others. This unique nature of children enables human civilization to build upon past experiences. Children, who accept the words of adults as rule of thumb, as “Don’t go to cliff of the roof”, “Don’t swim into the deep water” or “Don’t go to the forest alone”, are more likely to survive and reproduce later. When grown up, they propagate their memes, accumulated in the childhood to the next generation, and may be in a modified format. The memes that are more appealing tends to propagate more accurately than the others.
Religion as a Memeplex
Religion and the existence of God as a set of memes have got the unique appeal to human civilization. It provides plausible answers to deep and troubling questions of the nature, suggests the ‘injustice’ will be rectified in the next and one will be placed in relatively good or bad places after death depending on the performance in this life. Dawkins, in his book The God Delusion (pg 199) has provided a list of religious memes those had high survival values in human civilization.
The reasons for the high survival of religious memes include social experience, speculations and distinct source. The religious people always express their experience as positive to add the survival value to the meme, e.g. faith is a virtue and prayer is the way to seek help from God. People speculate about mysteries of nature, miracles, life and death that ensure high survival for the religious explanations. Last but not the least, the revered and distinct source (religious leader/book) adds additional survival value to it. Presence of ‘exclusivist’ memes in the organized religion is striking. For example, punishment or ostracism for heretics, apostates and blasphemers are such ‘exclusivist’ memes. These memes protects the memeplex to get infected from ‘outsider memes’. One of the distinct features of Indian culture is the lack of ‘exclusivist’ meme, that enables India to be built on top of a unique plural society.
A reflection on the above theories can provide you clues why religious sects exist. Sects came into being due to different variation of ‘interpretation’, resulted out of different memetic evolutionary path followed by different sects. Same way, the recombination of different memes resulted in same religion to be performed in different ways in different regions.
The Roots of Religion
As we know how religion and the features propagate, we can proceed how it came into being initially. The best explanation, although controversial, I have got is from Daniel Dennett, in his book The Intentional Stance. He classified the stance of human beings with respect to an object in three ways – physical stance, design stance and intentional stance. In a Physical stance, man tries to explain the object and its’ behavior in terms of natural laws. The second one is design stance, to predict the behavior of the object as it is designed to perform that, e.g., the bird flies by flapping the wings or an alarm clock is designed to ring at a particular time. This is in effect a shortcut over the earlier one and provides advantages if established upon experience. The last one is the intentional stance, that enables personification of the object and predict the behavior as per the intention of the object. The intentional stance, very frequently gave humans advantage over other animals e.g., to identify predators (like Tiger) and cattle (Dogs). The noticable point is that the abstraction of objects is increasing in each stance. The human civilization is basically a race from the third one to the first – initially they had to take the more abstract ones due to lack of knowledge to go to physical stance. Dennett argues that it is best to understand human beliefs and desires at the level of the intentional stance, without making any specific commitments to any deeper reality to the artifacts of each and every folk psychology. The gods and the God, along with the Angels and Daemons are nothing but these personifications of these objects – survived in human societies as memes.
The Future
The clash of reason and religion is basically the clash of memes. The memes of reason are supported by evidences, those a human being can directly experience. The memes of religion are appealing and has high propagation value. The battle is likely to continue in future.
Conclusion
A memetic view of religion is undoubtedly better than any view proposed by the popular religions as the ‘first cause’ or the beginning of themselves. The explanation gives us idea on how the simple ‘personification’ of unknown objects turned into what we see as organized religion, by means of propagation of memes. The hypothesis, may have a lot of technical drawbacks, but overall is very effective in this case.
References
A bibiliography on meme.
The multi-dimensional evolution.
Susan Blackmore and her “The Meme Machine“.
The Selfish Meme – a concept.
Intentional Stance made easy. Also from the blog , book and video.
A New Planet in the Horizon
I think that by now everyone has added a new name in the General Knowledge memory – Gliese 581 c. It’s not only the name of a newly discovered planet having an environment similar to that of Earth, but also is synonymous to an ongoing threat to remove Humans and their beloved Earth from the center of life-creation.
It was long believed in ancient and medieval ages that the earth and human beings are special creation of God. Galileo and his follower Charles Darwin has broken into that house of faith with a powerful set of observations. While Galileo removed Earth from the center of the Universe, Darwin put humankind back to the nature, just another species evolved in a complex natural process.
Coming back to possibilities of life outside the Earth, one can divide the approach in two different steps. The first would be to search the Earth-like planets, in the ‘Habitable zone‘, the next could be the search for life on the planet. Only when the step one is confirmed, people generally look into the step two.
While the existence of ‘intelligent life’ in our Solar system is almost (Science really cannot disprove anything) impossible, the search for the preliminary form of life is still on. The best bet on this topic is possibly Europa, the ‘moon’ of Jupiter. It has a hypothesized ocean beneath its icy surface, which is supposed to contain life. It also has Oxygen in its atmosphere. The same kind of life might be present in Ganymede and Callisto. Jupiter and Saturn could have been a destination of Ammonia based life as hypothesized by Carl Sagan. Besides, NASA reported strong evidence of getting life in Mars.
The extra-solar planets are still open to all kinds of life possibilities. That is why the discovery is such an important milestone in Search for Extra-Terrestrial Intelligence. However, these planets are detected via some indirect method, hence the confidence attached to the properties of the planet discovered is considered low.
On 24th this month, Scientists at the European Southern Observatory in La Silla, Chile claimed they had found the first Earth-like planet. The planet orbits within the habitable zone of Gliese 581, a red dwarf star which is a scant 20.5 light years from Earth. If oxygen or methane (tell-tale biological gases) are found in Gliese 581c’s atmosphere, this would be good circumstantial evidence for life. Dr Malcolm Fridlund, a European Space Agency scientist, said the discovery of Gliese 581c was “an important step” on the road to finding life. Interestingly, Gliese 581c is so close to the Earth that if its putative inhabitants only had our level of technology, they could – just about – pick up some of our radio signals, such as the most powerful military transmitters.
One could remember the famous Franc Dreck equation to find out how difficult it could be to find an evidence of life on the Earth. It is not only extremely difficult, it costs a lot also. Due to lack of funding, a lot of projects could not take off in recent years. However, the importance of such a project can never be undermined. It would help us to identify how the life grows, or possibly what the life actually is. May be, also to create new form of life.
The Origin of Life : RNA Hypothesis
Of late I have been reading books by great scientists. The best one as I found out, is one from James Watson, named as DNA : The secret of Life. I have gone through first three chapters of the book only. It has given me a lot of knowledge on how the life has been evolved on the earth.
The basic mystery that I had prior to reading the book was on the relation between protein and life. The explanation that I got is really interesting. It’s the DNA that replicates a part of it (transcribes) to messenger RNA. The messenger RNA then comes to Ribosome and gets translated to amino acids with the help of transfer RNAs present there. Amino acids are catalyzed by RNAs to build polypeptide bonds among them to generate Protein. But, DNA, RNA and the Proteins are built on nucleotides.
Here the RNA World hypothesis comes into picture. It’s now obvious that RNA has a property to store, transmit and duplicate the genetic information as DNA. It can also produce proteins – the building block of life. According to this hypothesis, RNA was independent initially and later evolved a barrier outside to form later form of life – like bacteria and Amoeba. Carl Zimmer, who’s working on this for long, believes that RNA Viruses are the last common ancestors of life. They evolved into DNA based viruses and since then, the superior system of DNA based life exists.
The most interesting part to me was the role of Natural Selection in the process of forming RNAs. Initially nucleotides (purely chemical substance) were free floating. They were often formed bonds to bind together. but certain sequence of bonds had properties to bind and go to more stable state. As each chain grew longer it attracted more matching nucleotides faster. RNA is one of these giant nucleotide chains. In an RNA world, different forms of RNA compete with each other for free nucleotides and are subject to natural selection. The most efficient molecules of RNA, the ones able to efficiently catalyze their own reproduction, survived and evolved, forming modern RNA. The competition grew and resulted in co-operation between separate RNA chains to produce more and more different proteins. DNA came later and so lipids, carbohydrates and other materials since a collaboration of such materials were more ‘sustainable’ and ‘replicable’.
The main problem of this thesis was the instability of RNA while being exposed to UV Rays. Recent experiments also suggest that the original estimates of the size of an RNA molecule capable of self-replication were most probably vast underestimated, the size can be smaller than one have thought of. More-modern forms of the RNA World theory propose that a simpler molecule was capable of self-replication (that other “World” then evolved over time to produce the RNA World). There are many more hypothesis surrounding this RNA and life but the lack of undisturbed sedimentary rock from that early in Earth’s history leaves few opportunities to test any of these hypothesis robustly.
The idea of RNA world was first proposed in Carl Woese’s The Genetic Code. The term was coined in 1986, by Walter Gilbert.
The origin of life on earth is a mystery that Humankind ought to solve. The proper understanding might give us several advantages over the natural world. We may create our own microbes to fight against the diseases caused by virus and bacteria. We will have much better understanding of each of the building blocks of our own body.
News Reference from BBC :
Creation of Viral life by researchers.
