tag:blogger.com,1999:blog-20193006880749472042024-03-19T06:02:57.309-07:00Notebook of Small IdeasBy Deepak ChandranDeepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.comBlogger42125tag:blogger.com,1999:blog-2019300688074947204.post-49253777434988517082016-02-12T22:28:00.000-08:002016-02-14T16:31:27.435-08:00Trust in Synthetic Biology<div dir="ltr" style="text-align: left;" trbidi="on">
The concept of <i>trust</i> with respect to synthetic biology has enormous economic importance. Lack of trust can cause people and governments to block an entire division of research, such as GMOs in some parts of the world. Similarly, synthetic biology related companies that have lost their reputation can have great difficulty releasing an honest product. Consider other products, such as an electronic device. Such products are often <i>tested</i> by unbiased individuals; the reviews generated by these unbiased individuals is trusted by the general public. By using such third-party reviewers, who share their testing methods openly, a product is able to gain trust on its own. <br />
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The review process for biological or chemical products is different. The processes of assessing safety and effectiveness of medicines, farm-related products, and various chemicals for every-day use are often hidden in publications that are normally difficult to understand by the users. Websites that target the general public often rely of vague concepts rather than specific facts. What if biologically engineered products had a review process that is open. <br />
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"Open" is not a matter of exposing the raw results of experiments. Open must allow other individuals to repeat the tests and contribute their results. Open must also mean that honest efforts have been made in order to make the information understandable by as many people as possible. Open access to scientific publications does not mean that the knowledge is open because those publications are generally written for domain experts. Further, publications do not guarantee that the experiments are reproducible. In order to address the problem presented in the first paragraph of this blog, open-science needs to invent a new method of sharing information.<br />
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Additionally, trust is often strengthened when both sides are involved. If customers of a product participate, even remotely, in the testing of the product, their trust, through a feeling of ownership, is likely to increase. For example, suppose some of the customers utilize open labs in order to conduct some of the verification experiments. It would cause the customers to feel a bit closer to the product.<br />
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Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-5319134811763245192015-07-06T09:48:00.001-07:002015-07-06T09:48:13.375-07:00Morning Dew<div dir="ltr" style="text-align: left;" trbidi="on">
Morning dew hanging from the railing of a balcony - I looked at them for a while. As I noticed the details, it was only natural to think about the geometric shape created by the droplets and the Poisson distribution of the droplets along the rail. Someone versed in music might imagine a song. A poet might invent a new poem. All are expressions of appreciation of morning dew. There is a feeling associated with this appreciation of nature. When I have this feeling, I cannot imagine how science or art can exist without that feeling. It is simply the foundation for science or art. Science education that does not exercise this feeling is education without the foundation of science.<br />
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Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-63047405365661136932013-07-25T22:21:00.000-07:002013-07-25T22:21:42.941-07:00Cancer cells might be Creative<div dir="ltr" style="text-align: left;" trbidi="on">
I have heard a few times that human beings are comparable to cancer (not a positive view, sorry) in the sense that humans: (1) drain resources from the other members of an ecosystem, (2) grow at a disproportionately high rate when compared to fellow animals, and (3) cause ecosystems to malfunction due to the previous two behaviors.<br />
It can also be argued that human beings have their advantage due to the combination of a creative brain and social skills. Physically, human beings are hardly a match for most other animals. So, taking this analogy back to cancerous cells, would be appropriate to say that cancer cells have a sort of "creativity" that is lacking in other cells. Just as a "better" brain is defined by the amount of information it can process, it is arguable that cancer cells process more information than other well differentiated cells, partly because cancer cells can perform a myriad of functions. </div>
Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com2tag:blogger.com,1999:blog-2019300688074947204.post-3101604800976111912013-06-22T13:29:00.002-07:002013-06-22T13:29:43.027-07:00Synthetic Biology vs natural biodiversity<div dir="ltr" style="text-align: left;" trbidi="on">
A constant worry in the environmental front of synthetic biology is its influence on natural biodiversity and natural systems in general. Synthetic biology products are human-made things, no more natural than buildings, radio, or television. If this is the case, the question about environment is not solely related to synthetic biology but engineering as a whole. Human constructions - buildings, roads, night lights, irrigation, dams, etc. - have probably affected natural systems significantly. Synthetic biology is another item on this long list; perhaps humans were much less careful about natural systems when they first started engineering buildings or dams. After witnessing the slow decrease of natural landscape, perhaps humans have become more cautious about consequences of engineered products. The question on how to safeguard natural systems from engineered biological systems is perhaps a starting point to the question about how to safeguard natural systems against any engineered system.</div>
Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-7840240632063770322013-03-04T16:41:00.000-08:002013-03-04T16:41:10.696-08:00rules in biological systemsResearchers are often surprised when we find organisms that break the 'rules' of living systems. These rules include commonly observed phenomena such as amino acid codes, conserved metabolic pathways, etc. Considering the unplanned nature of evolution, it should be surprising that such rules actually exist. It should feel more logical when rules are broken.Well, lets consider other places where we find 'rules'. Human societies have rules, and even though every person has different interests and tastes. People agree on the rules because what is gained from following the rules is probably greater than the gain from breaking the rules (in general). Similarly, perhaps rules exist in living systems because there is sufficient gain - better exchange of information between organisms, better 'modularity' in evolution, role for viral-mediated horizontal gene transfer, etc. Now, the question to ask is - what does it mean when organisms break the roles? Perhaps they belong to a different society with a different 'culture', or perhaps they are lone explorers who do not want to interact with the rest of the system.Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-14205969381118651442012-11-04T06:16:00.001-08:002012-11-04T06:16:37.724-08:00The ideal biofuel company...<div dir="ltr" style="text-align: left;" trbidi="on">
The ideal biofuels company would not use giant farm land to produce large amounts of fuel for everyone. Rather, the company would sell barrels to people. People can put any compost-able items (left over food, paper, maybe human waste, etc) into the barrel. The microbes and/or other chemicals in the barrel would convert these items to fuel, making people self-sufficient. Of course, people who do not have a back yard would probably have less material; for these people, the company can sell fuel made from waster matter that is purchased from other people who have excess waste.<br />
The big question is regarding efficiency - whether waste material from individual homes would provide sufficient fuel. But even if it provides a certain fraction of the fuel requirement, that is still a significant step. </div>
Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-53589415465030872172012-10-12T12:41:00.000-07:002012-10-12T12:49:57.443-07:00Analogy for Cancer as a Systemic Disease<div dir="ltr" style="text-align: left;" trbidi="on">
Lets think of a multi-cellular organism (i.e. humans) as a small city, a society, of individual cell citizens. When the citizens of a society feel a strong sense of unity and like to interact with one another, the chance of someone becoming malicious is small. Any malicious person is likely to get caught because the members of the society have a high rate of interaction; members who interact in an unhealthy way would be identified quickly. On the contrary, in a system where individuals are isolated, it is quite easy for a malicious individual to remain hidden and carry out their plans.<br />
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Carrying over the analogy to the human body, the "malicious citizen" is the cancerous cell. It is not an invader but a member of the system. Now the question is: what creates a sense of "unity", or high level of interaction, in a multicellular system? This question is difficult to answer even for a human society - what creates a sense of unity in a society? The answer might lie in vague concepts such as culture, language, values, or beliefs. These are abstract concepts. Concepts such as culture cannot be written into books; they evolve; they form spontaneously and are not designed by humans.<br />
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So the task is to identify what constitutes the "culture" of a multicellular organism. My imagination tells me that the answer might lies with wave-like patterns within the body - heartbeat, breathing, hormone cycles - that affect almost all the cells in the body. The fact that these phenomena are oscillations allows cells to synchronize, or resonate, with those patterns. Multiple waves can combine to form more interesting patterns. Cells resonating with this pattern might be in similar physiological states, and therefore, those cells might interact with one another more. More interaction creates a healthier "society".<br />
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If the above hypothesis is true, the way to heal a large number of illnesses lies in identifying patterns of global phenomena such as breath, blood flow, hormone cycles, and especially how they interact with one another to form more information-rich wave pattern(s). Then, we can identify how various cells change states in response to this global pattern. <br />
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In some sense, malicious members of a society are like indicators of the society's overall health. In an unhealthy society, more individuals would feel less inhibited to harm one another. In this sense, the malicious members ensure that an unhealthy society falls apart, giving way to a new, healthier, society. Cancer might serve a similar purpose. A body where the overall unity is weak is perhaps dangerous to the larger ecosystem. Cancer ensures that such a system falls apart.<br />
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Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com1tag:blogger.com,1999:blog-2019300688074947204.post-53534320830548450232012-10-12T08:59:00.001-07:002012-10-19T10:53:39.810-07:00Analogy connecting Proteins to Words in a language<div dir="ltr" style="text-align: left;" trbidi="on">
While analogies can be dangerously inaccurate at times, they can also be invaluable in other cases. Therefore, they are worth considering (with open-minded skepticism). So, here is an analogy of molecular biology research...<br />
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There are 26 alphabets in the English language and 20 amino acids (maybe more) in biological systems. Combination of these basic alphabets can be used to constructs hundreds of thousands of words, and similarly, combinations of amino acids can be used to create numerous different protein molecules. However, both are retrained in some way. For example, when constructing a new word, we will probably not create something like "qxtrpeeoo", because it is not speakable. Similarly, when making protein molecules, stitching together random amino acids would not produce a stable molecule in its environment. So, there is some similarities.<br />
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Now, lets try performing some "experiments" on words in a similar way that we do experiments in biological systems. Lets try a "kockout" experiment. We will remove the word "grocery" from all text in a city. We might see that traffic patterns have changes because people are trying to find grocery stores. After a few weeks, people adjust to the situation, so the traffic patterns settle. So, from this observation, what might we conclude about the role of "grocery" in society? Consider a different experiment in which part of a word, e.g. prefix or suffix, is removed or a different part is added. What type of conclusions would we reach by observing the consequence of such changes?<br />
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So what is a different approach to learning the meaning of words? I do not have an obvious answer, but following the above analogy, one might look at how babies learn language. First, they usually learn words that refer to real objects, such as "light" or "fan" or "mom". Applying this analogy to proteins, it might be reasonable to start with proteins that directly interact with the environment, e.g. binds metals or other environmental signals (i.e. objects outside the internal language of the cell). Moving from the word "light" to the meaning of a sentence such as "the light is on" or something more intricate such as "please turn the light on" is a much larger step because here the word "on" is entirely context dependent. The same word would mean something entirely different in a different sentence. It is possible that some proteins, specifically those involved in internal signal processing of the cell, are entirely context dependent. Consider the difference in the response when someone asks "is the light on" vs "light is on" vs "turn the light on". All of these involve "light" and "on", but the response of the listener is quite different in each case. <br />
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Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-86481540378059558232012-08-21T15:14:00.001-07:002012-08-21T15:14:23.513-07:00Distributed research...(again)<div dir="ltr" style="text-align: left;" trbidi="on">
Imagine if we have two things:<br />
1. public research labs such as the BioCurious in many cities<br />
2. free software system for uploading pictures, data, etc. from experiments<br />
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Then, a situation such as this can be possible:<br />
- person A starts an experiment on day 1<br />
- person B comes to the same lab, looks up what remains to be done for the experiment and performs the remaining steps on day 2<br />
- person A comes back and uploads pictures of the results, e.g. gels, plates <br />
- person C, located across the world, sees the pictures, analyzes them, and uploads the analyzed data<br />
- person D, watching the experiment from some other location, makes some insightful observations<br />
- and for the sake of practical benefits, persons A-D, having demonstrated their caliber, get recruited to an excellent university/company.</div>
Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com1tag:blogger.com,1999:blog-2019300688074947204.post-42645564389280619402012-08-04T15:52:00.002-07:002012-08-04T15:52:40.792-07:00Environmental sensing by the collective<div dir="ltr" style="text-align: left;" trbidi="on">
Imagine if everyone who scoops up a cup of sand, lake, or ocean and submits it to a local repository gets some money in return. Why? Well, the local repository would process the microbial population and make it available to the public. Companies can analyze this data and predict changes in climate, spreading of potential parasites, etc.<br />
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Further, rather than analyzing microbes, it might be even more informative to analyze bacteriophages. First, they are more diverse than bacteria. Second, phages generally switch between dormant and virulent states based on environmental factors, hence providing an additional source of information.<br />
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<br /></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-43204086338917362632012-02-06T11:26:00.000-08:002012-04-06T21:15:44.982-07:00The wet-lab machine<div dir="ltr" style="text-align: left;" trbidi="on">
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<b>Problem</b>:</div>
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Scientific literature is openly available to anyone who wants to read them. However, "open" does not mean much if no one can understand them. Molecular biology protocols fall in this category. If you are not a molecular biologist, you will probably have no idea what the "methods" section of a molecular biology journal paper is talking about.</div>
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<b>Possible solution:</b></div>
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The Incredible Machine is a nice game that is fun and intellectually challenging. For how complex the scenarios are, the interface and visualization make the game relatively simple to learn. </div>
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<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.youtube.com/embed/kl7hT2GiO5E?feature=player_embedded' frameborder='0'></iframe></div>
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I wonder if an interface like the incredible machine can be used to explain wet-lab procedures. Of course, the minute details would not be illustrated, but one of the issues with wet-lab at present is that there are only protocols. There are no higher-level 'big picture' explanations, which are necessary for someone who is trying to learn how to do wet-lab. In some sense, there is nothing equivalent of a pseudo-code.<br />
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<b>Imagine supplementing the "methods" section of a journal paper with a cartoon animation similar to the Incredible Machine</b> - how much more education value would it add to the journal paper! Further, imagine a repository of Incredible-Machine-line animations explaining the overall ideas behind wet-lab protocols. </div>
</div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com1tag:blogger.com,1999:blog-2019300688074947204.post-71858404049187614772011-12-16T09:21:00.000-08:002011-12-29T17:09:06.957-08:00Perfect class project for teaching science<div dir="ltr" style="text-align: left;" trbidi="on">
Imagine a class project where the students have to find a few failed experiments (or experiments with confusing results) and develop hypothesis on possible explanations. Of course, some of them might be human error, but that is the part of the challenge of the assignment -- to develop reasons why that is the likely explanation.<br />
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I don't think this assignment is possible at present. Why? Below are my reasons, although I am sure there are many more.<br />
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1) There are a few journals of negative results, but I think they probably capture only a very small fraction of the number of failed experiments [in biological sciences as a whole].<br />
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2) EVEN IF all the failed results were published, how would a student navigate through them. Usually, understanding the nature of a failure is far far more difficult that understanding a successful experiment, because the pieces of a successful experiment make a coherent story. For a failed experiment, an expert in the field is often required to hypothesize potential explanations.<br />
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<a href="http://www.clker.com/cliparts/s/v/Z/0/L/E/confused-panda-hi.png" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="200" src="http://www.clker.com/cliparts/s/v/Z/0/L/E/confused-panda-hi.png" width="191" /></a>3) Failures MAY very often relate to each other. I, personally, think that most failed experiments can be attributed to a combination of human error and actual biological issues. If this is true, then looking at any single failed experiment is meaningless (sort of obvious). Finding "patterns" amongst thousands of failed experiments is practically impossible via the traditional journal-reading process.<br />
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<span class="Apple-style-span" style="color: #0b5394;">Possible solutions (ambitious):</span><br />
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I believe that the human eye is extremely efficient in finding patterns, and therefore, it is necessary to leverage the visual + intuition capabilities of human researchers in order to make sense out of failed results.<br />
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A class project means that this task needs to be accomplished by non-experts. I think a framework that combines education + research + visual representation of results can by-pass this problem. In other words, provide ways to educate a student about a method when presenting the results from that method. If such a framework can be created, the boundary between education and research may become vague, which might be quite remarkable.<br />
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<span class="Apple-style-span" style="color: #0b5394;">Implications:</span><br />
<br />The traditional test-based system for selecting students is bound to miss several great minds who have the potential to solve many unresolved mysteries in science. If an infrastructure can be constructed where anyone can educate themselves and connect research results efficiently, there is a possibility that various geniuses around the world will be able to utilize their potential and service the community. The opportunity to circumvent the traditional test and money-based avenue to higher-education should provide an incentive for students around the world to try to do science on the side. <br />
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<br /></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-81281761209903426352011-12-08T19:43:00.001-08:002011-12-08T19:51:11.892-08:00Leave "pheromone trails" on research articles<div dir="ltr" style="text-align: left;" trbidi="on">
What if there was a way to leave a "trail" (like ants) whenever researchers jump from one research article to another and find the connection very interesting. As more researchers walk the same path, the "pheromone" along that trail becomes stronger. This would provide a nice way of linking interesting research articles together, highlighting interesting patterns in the network of related research papers.<br />
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<br /></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-40145168658479889012011-12-07T09:35:00.000-08:002012-07-27T13:30:02.661-07:00A dynamical systems analogy of society<div dir="ltr" style="text-align: left;" trbidi="on">
Lets consider individuals in a human society as monomers. These monomers can interact in different ways to form larger complexes, with each complex having different functional capabilities. The reason why monomers might come together may be different. For example, in a modern company of workers, the monomers come together because of money - the salary provides the attractive force that brings the monomers together to form a larger cluster. Families are formed due to a different form of attractive force. Friends circle and so on have a different (maybe similar) force. Non-profit organizations or other occupations that are not motivated by salary (i.e. intrinsic reward based systems) attract monomers for an entirely different reason. I think this type of attractive force forms a larger variety of complexes, many of which interact more closely with the world outside human society (based on a few observations).<br />
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Now, lets consider society as a system with multiple stable states. Each stable state is defined by the types of complexes that exist in that state. For example, in one stable state, all the complexes are formed by salary-driven forces. In another stable state, the salary-driven forces are weak and therefore, intrinsic-reward forces are responsible for forming complexes. In another stable state, perhaps other forces are responsible for the complex formation. The question is: what causes these systems, i.e. societies, to shift from one state to another?<br />
<br /></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-4191572319000084982011-09-13T19:53:00.000-07:002011-09-13T19:53:33.702-07:00Yet another perspective on evolution<div dir="ltr" style="text-align: left;" trbidi="on">
Consider this possibly true scenario:<br />
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Virus X lives inside 10% of the human population. It has integrated itself into the human genome, as many viruses do. It gets activated during the lifetime of a human and it exists the human body through the mouth and nose It is only able to invade other humans with specific proteins, which happens to be the same 10% of the population. In addition, this virus is also able to invade 10% of dogs and cats.<br />
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In the above situation, the virus X serves as a channel for DNA exchange. In other words, it is possible to build a "family tree" based on this virus. It is another a family tree based on a different means of reproduction. In normal reproduction, we do not reproduce our entire selves. Rather, some part of us is reproduced. Virus X is also reproducing a small part of us, and therefore, it is just like normal reproduction.<br />
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We think of the "tree of life" as a tree with lots of horizontal transfers. What if all these horizontal transfers actually form another tree of life, a tree that uses a different means of reproduction. Why limit to viruses? Microbes in our body are part of us. If microbes are mutating and being carried between species, then they, too, can be a means of reproducing a part of us. In summary, there might be several means by which we reproduce specific aspects of "us". Each of these means of reproduction can be used as a basis for building a different "tree of life". All these trees intersect.<br />
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So what is a species? It is basically a way of categorizing individuals. Just like there are different ways to classify books (e.g. language, subject, readers), there are different ways of classifying individuals. Each individual belongs in <i>multiple</i> species -- one for each type of reproduction process that affects the individual. We are all part of more than one species. So why do we give the regular form of reproduction so much importance? It's because of the brain, of course. The brain is not the master of our body. It is one component of the body, and just like any other component, it has roles. The brain is designed to pay attention to certain types of reproduction. For humans, these types of reproduction include sexual reproduction and cultural (meme) reproduction and maybe some other ones. We should not let the role of the brain affect the reality, which is that all of these forms of reproduction contribute significantly to natural evolution.<br />
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Therefore, natural evolution is a process where multiple trees of life are expanding and interacting. Individuals sit at the intersection points of these trees.</div>
Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-10989897034581364002011-08-31T16:02:00.000-07:002011-12-16T09:24:55.960-08:00Crowd science<div dir="ltr" style="text-align: left;" trbidi="on">
First of all, the two problems being addressed...<br />
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1) Great ideas are created when several small ideas come together. The<br />
inability to keep up with a wide variety of research will lower the<br />
chances of small ideas coming together. We're having trouble keeping<br />
up with publications in just our own field, so imagine what all useful<br />
discoveries we might be missing from other fields, especially those<br />
obscure journals which might be hiding fragments of a great discovery.<br />
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2) Currently, if a curious high school student wants to learn more<br />
about ongoing research, they would have to start reading review papers<br />
or something like that -- this is not very inviting. No wonder the gap<br />
between researchers and public is growing. The current mode of doing research requires a person to go through the PhD 4-6 year ritual. A self-motivated individual does not have sufficient material to become a self-motivated scientist. Even worse, a scientist who wants to cross from one field to another also needs a cross several large barriers. <br />
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And now, the solution...<br />
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An online game. Imagine a role-playing game where you walk around on<br />
the earth (google earth-like interface with a person walking on it).<br />
As your character walks through regions of the globe, you will see<br />
little signs pop up indicating where the research labs are. There will<br />
also be signs for "schools" (described later). When you click on a<br />
research lab, you see comic strips of up-to-date research -- that's<br />
right, comic strip of what each post-doc, graduate student, and<br />
faculty did that day or any other day. You will also see the data<br />
(graphs, tables, etc.) below each block of the comic strip.<br />
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Each comic strip is one line. It starts with a 'mission statement'<br />
(objective or hypothesis) and ends with a concluding statement.<br />
Conclusions can include emoticons, of course. Everything between those<br />
two sentences describes what was was done using pictures and short<br />
descriptions. The comic strips would describe procedures like miniprep<br />
and PCR or even computational steps like parameter fitting. The player<br />
can hover over the comic strip and find "schools" that teach those<br />
concepts. E.g. I would hover over "PCR" step and see several schools<br />
located across the globe that teach what PCR is, with ratings for each<br />
school. Clicking on the schools takes me to online lessons (videos,<br />
etc.) that teach those concepts. Schools with high ratings might even<br />
make money from ads (incentive).<br />
<br />
Ok, so now you ask how will these comic strips be generated... with<br />
the Comic Maker of course! Each research lab participating in this<br />
game can download a software called Comic Maker. Comic Maker comes<br />
with hundreds of comic blocks representing some basic procedures. Each comic block can be generates by combining those basic blocks. It will have an easy drag-n-drop interface for creating a pipeline and attaching data to each step of the pipeline. The researcher must start a pipeline using a 'mission statement' and end it using some conclusion, even something as simple as :-( or just a few key words.<br />
<br />
More fun stuff: researchers can announce "quests", which are open<br />
problems that they are unable to resolve. Gamers can get involved in<br />
quests. These players have to gather facts from other labs across the<br />
world and generate some solution. They can request the researcher to<br />
perform new experiments for them if they need more data. Similarly,<br />
gamers can create novel hypotheses by collecting results from several<br />
pipelines and present them to researchers.<br />
<br />
One key question is: how does this reward the scientists who are in universities? Mainly, the reward is visibility, which is in many cases a big reward. Making research visible is a key for doing good research, and most researchers understand this obvious fact. Of course, placing results in this online game might interfere with the current "publications" approach. The workaround for that problem is simple: just place this in the game after they are published. <br />
<br />
<br />
That's it. Hopefully that was a fun read. I think it can can be done.<br />
Imagine spending your weekend looking at comics of what everyone is<br />
going at Berkeley instead of going through the procedure section of a<br />
paper. Of course, there will be nice search features, like "find me<br />
everyone who is doing XYZ", where "XYZ" is some sequence of<br />
procedures.<br />
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<a href="http://www.library.drexel.edu/blogs/groupwork/files/2011/09/CLIPART_OF_16323_SM_2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="http://www.library.drexel.edu/blogs/groupwork/files/2011/09/CLIPART_OF_16323_SM_2.jpg" width="320" /></a></div>
<br /></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com2tag:blogger.com,1999:blog-2019300688074947204.post-48098954472202898052011-08-19T10:08:00.000-07:002011-08-19T10:09:54.791-07:00Information vs information carrier<div dir="ltr" style="text-align: left;" trbidi="on">Suppose I write the word "Mango" using pen and paper. Then, suppose I wrote the same word using a chalk and blackboard. It is obvious that I am conveying the same information. The instrument used to convey that information is hardly relevant.<br />
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If this analogy can be applied to biological systems, then it is misleading to study physical aspects of signaling separately. Whether the signaling is via transcription factors, enzymes, RNA molecules, small metabolites, or DNA structure, there may not be any relevance with the content of the information that is being delivered by those molecular interactions. Similarly, between-cell communication may not be related to the type of signaling (paracrine, endocrine, quorum sensing, etc.). It might even be possible that the information encoded by molecular interactions is no different that information encoded by cellular interactions.<br />
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In summary, it is possible that information in biological systems might come to light if we study the patterns and ignore the physical components that create those patterns. At the same time, the physical aspects are not completely irrelevant. One would not write a book using chalk and blackboard, so the physical aspects of the instruments do restrict the type of information that can be conveyed.<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="http://www.miqel.com/images_1/fractal_math_patterns/natural-patterns/fractal_bacteria_colony_3.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="http://www.miqel.com/images_1/fractal_math_patterns/natural-patterns/fractal_bacteria_colony_3.jpg" width="316" /></a></div><br />
</div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-52409837677405048602011-08-10T10:24:00.000-07:002011-08-10T10:24:34.515-07:00Cell density based effects<div dir="ltr" style="text-align: left;" trbidi="on">In videos such as the one below, the cells in the middle have smaller size and therefore, there are more cells per unit area. This means that the concentration of molecules inside those cells might be different from the concentration of molecules in the cells at the outer boundaries. Suppose the cells have multiple stable states; in such cases, concentration differences can trigger state changes, causing different behavior of the cells based on their location in the colony.<br />
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Colonies where density is not equally distributed might use this fact (density dependent state change) to create different roles within the colony. Maybe the state of the cells at the center governs certain aspects of the colony and the state of the cells at the edges governs some other aspect of the colony. Even if evolution has not used this observation as a design strategy, it does not limit us from using the density difference as a design strategy for creating diversity within a population.<br />
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</div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-80759908229900856932011-06-26T12:11:00.000-07:002011-06-26T12:11:50.748-07:00Unnoticed evolution of humans<div dir="ltr" style="text-align: left;" trbidi="on">1) Suppose that the microbial community living inside us have a sufficiently long relationship with our own cells such that the microbes have an important role in a large majority of physiological functions, not just digestion.<br />
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2) As human societies have evolved, the variety of microbes that live in our environment have undoubtedly changed. Once humans wandered grasslands on bare-foot and ate raw food without even washing them. Now we buy processed food from supermarkets and even walk inside our houses with socks. The result is that the community of microbes that interact with and enter/exit our bodies has changed.<br />
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Combining (1) and (2) above leads to the possibility that the human physiology has indeed changed of the past several centuries, even though the change the human phenotype "appears" unchanged. The extent of evolution depends on the extent to which the microbial communities influence human physiology. If there are long-distance signaling molecules that are released by microbes which enter the blood and if the microbes are capable of receiving our signals, then...<br />
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</div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-81543952548491303792011-04-22T16:21:00.001-07:002011-04-22T16:46:51.907-07:00Analogy for Protein Bursts<div><b>Consider this scenario:</b></div><div>Imagine a store that is open for a certain time interval during the day. In that time interval, several customers rush in to the store. Each customer buys several items. If someone would record the number of items sold as a function of time, he/she would probably observe bursts (one burst = items bought by one person). The time duration for which the store is open will correspond to the <i>number</i><b style="font-style: italic; "> </b>of bursts. In other words, time duration maps to frequency of bursts. </div><div><br /></div><div><b>Now, consider this transcription model:</b></div><div>Consider this mechanistic/intuitive model explaining how proteins are produced in bursts and how the frequency of bursts are controlled by the transcription factor:<div><br /></div><div>1. transcription factor binds to promoter regions and opens the region for access by the polymerase</div><div>2. the region remains "open" for some time</div><div>3. during this time interval, the polymerase may initiate transcription multiple times</div><div>4. for each mRNA that the polymerase transcribes, multiple proteins are produced</div><div><br /></div><div>So, in summary, the transcription factor "opens" the promoter region for the polymerase. Lets assume that upregulating the transcription factor affects the time duration of the "open" promoter. The longer the time interval, the more mRNA will be produced. Each mRNA creates a burst of proteins. Therefore, upregulating transcription factor affects frequency of bursts. </div></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-14760649875736137342011-04-22T16:12:00.000-07:002011-04-22T16:55:06.980-07:00Stochasticity can lead to StabilityWhile we think of "noise" as a destabilizing force, we actually use noise many times to lead a system to the most stable position. Consider the scenario where you want to get all the items out of a hand bag very quickly; you would hold the bag up-side-down and shake, i.e. add noise. If you just tilt the bag up-side-down, there is a risk that some of the items would get stuck in the bag. Shaking ensures that such temporary "traps" (in mathematical terms, local minima) are avoided. In a sense, this is like stochastic optimization. When all the items are on the floor, they will remain there even if you shake the floor, because that is that is the most stable position. <div><br /></div><div>Perhaps stochasticity in natural systems is a means of "shaking", i.e. a means by which natural systems reach the most stable states and avoid local traps. The most stable state remains relatively stable even at the presence of noise. Consider the situation when all the items from the bag are on the floor -- even shaking the floor would not change the situation significantly. Perhaps this is the nature of the "most stable state" -- it has a wide basin and thus can easily tolerate noise.</div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-51829626583862238912011-01-21T18:51:00.000-08:002011-01-21T19:24:56.693-08:00Centralized synthetic biology for the community<div><b>Vision: </b></div><div> Build a "fun" framework that would attract lots of young minds to ask interesting questions, engineer biological cells to answer those questions, and easily share their results and explanations with each other. </div><div><br /></div><div><b>Problem:</b></div><div> 1. providing the education to the masses... but I have some hope that young people are quite good are educating themselves, given the motivation</div><div> 2. Resource</div><div> 3. Safety</div><div><br /></div><div><b>Possible solution:</b></div><div>One or two well maintained centralized robots with a fun interface for entering experiments and storing/visualizing the results. This is very much possible, except that it is expensive. But if the benefit is large enough, it is possible that government and/or companies might solve that issue. </div><div><br /></div><div>But if such a programmable robot existed as a resource, I can imagine numerous researchers wanting to try new experiments and test new hypotheses. Since the data is centralized, there is a built-in benefit of data-integration, i.e. finding relationships between multiple experiments and drawing conclusions based on large number of experiments. It would be like a Facebook for biological experiments: everyone wants to dump their favorite hypothesis on it.</div><div><br /></div><div><br /></div><div><br /></div><div><br /></div><div><br /></div><div><br /></div><div><br /></div>Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-44522247547743196932011-01-20T10:27:00.000-08:002011-01-20T10:33:25.278-08:00Exercise as a general solution to living systemsI heard the statement a couple of times that places in this world with more cleanliness tend to have more auto-immune illnesses such as allergies. One can imagine that the immune system also needs to "exercise" from time to time, just like the muscles in our body or the brain.<br /><br />What if "exercise" is a more general theme? Perhaps every pathway in a living system needs some form of exercise (but not too much, of course). What if the error-checking mechanisms and all the other anti-cancer mechanisms in our body also need exercise... perhaps we can cure cancer by exercising anti-cancer pathways. Exercise against cancer would be very tricky. It would require producing small controllable (or self-limiting) tumors in our body from time to time. By doing so, the hypothesis is that the body's anti-cancer pathways would remain alert (well exercised). This might make the body better prepared against the real cancer or tumor.<br /><br />The same theme of exercise can perhaps be applied to achieve other goals, e.g. directed evolution of microbes.Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-68807114101645596422010-11-17T19:07:00.001-08:002010-11-17T19:13:47.875-08:00Possible functions to evolve using reaction networksHow would simulated evolution resolve the following challenges:<br /><br />1) Measure the variance (noise) of a signal<br />2) Measure the frequency of a signal -- can be related to (1)<br />3) Reverse of (1), i.e. increase noise based on deterministic signal (without affecting mean)<br />4) Reverse of (2), i.e. increase frequency based on amplitude of an input signal<br />5) Control the width of a bimodal distribution based on a deterministic signal<br />6) Adapt to an external pattern of events (i.e. learn cause-delay-effect relationships) purely through the reaction network -- this would probably be a combination of signal processing + memoryDeepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0tag:blogger.com,1999:blog-2019300688074947204.post-82881932188472878972010-06-17T13:10:00.000-07:002010-06-17T13:15:31.744-07:00Design by homologous recombinationEngineers have frequently used random mutations as a means of optimizing a protein or genetically engineered network. However, I don't think this is an effective optimization or design process. Planned mutations, such as the one used by the immune system, rely on homologous recombination rather than random mutations. Using recombination, we can plan the mutation events, therefore perform a much more predictable optimization. The optimization process can even be simulated computationally.Deepakhttp://www.blogger.com/profile/03551734046229466486noreply@blogger.com0