Activism (occurs once in a blue moon!)

Delenda SOPA PIPAque sunt!

This is the essence of the message. The freedom of information is represented by the flame and the ever-hungry forces that seek to stop it are visible as the menacing eyes. The light of truth and reason is being threatened even now by SOPA and PIPA, which will show the world an example of what America, previously the beacon of freedom and liberty truly thinks of freedom and liberty.

For a lot more information in a more serious tone, visit this web (despite the blatant invocation of Click Me Syndrome).

A note to all spambots trying to comment here:

All of you will be hanged, drawn, quartered, and pilloried.

Special sequences for those searching


Apparently, some people want the MASPERGERS*<->MLARGESPER* sequence back after I removed it following a period of dabbling in existentialist philosophy, which is a torture I wish only on those peers performing grave offenses against something I cherished. In any case, here they are:


Keep the fact that you cannot just dump it into a standard DNA translation engine and expect to see the pattern in mind. You have to translate it biologically, meaning that you start at the ATG and end and the TAR. Translated forwards and assuming a 100% translation by those constraints (and ignoring things like friction and potential jamming), you will get MASPERGERS*. Translated backwards, you will get MLARGESPER*, which is very close to an anagram. Finding out that no one else had done this example was almost unbelievable (and you may see the initial posts at WrongPlanet, the other WP, as a vanished signature).

Return to Biochemistry

Ach! Vae mihi! I was commissioned to construct a paper model of G. gallus catalase last year q3 and forgot about working on it until now! It is time to launch the almighty UGene with the alignment between the PDB of the cow catalase and the sequence (i.e. non-graphical) of the chicken catalase.

A brief look at the PDB entries reveals that the vertebrate with the most entries is the cow, B. taurus. There are some human models as well, but the ones available are erythrocyte catalase while the cow models are liver catalases, just like the ones used during the first laboratory assignment in AP Biology.

[If only Chimera was a bit more stable and had a better alignment interface. Ah well, UGene has a perfectly good one. Also, keep in mind the fact that I am using only B. taurus and G. gallus and H. sapiens sequences when I say anything is conserved.]

The initial 41 or so residues seem a bit less conserved. 1TGU reflects this with a somewhat chaotic arrangement with an unusual amount of coil. This is just sequence A, so it may be incorrect. Enabling sequence D and taking a cursory look at only the ribbons (without atoms), reveals that the initial helix is probably necessary for proper assembly of the enzyme. The loosest interval at the moment (to be verified against conservation later)  seems to be (16,22), although 16 and 17 would have to have fairly high helix propensities. What I previously thought was a practically non-essential coil seems to be the place where chain C binds to chain A, and hydrogen bond inference indicated that the two chains were bound relatively tightly through the interval (24,38). Perhaps, this simply indicates that the choice of amino acids for this component is less strict and easily adaptable. I doubt the heme-binding sites will be as loose.

Next, I compare the results to the alignments. I thought I must have deleted something, because the initial alanine in the PDB as seen in Chimera sequence viewer was absent. It probably matters less, because the residue itself is not visible. In any case, the crazy mix of colors that provided the bases [sic, pun not intended] for the conjecture above stops as early as about 21 (by now shifted to match the Chimera sequence numerically). In addition, the relatively conserved initial sequence seems to terminate at 14, which is quite close to 16 and probably explains the necessity of that particular sequence. For this purpose, similar amino acids were also considered, i.e. d-e, n-q, g-a, and the others. I see few differences until 40, in which there is serine (hydrophilic) in B. taurus but isoleucine and valine in the chicken and human catalases respectively. I will note this oddity when I reach the 156th residue. Perhaps, the serine is only a, “spacer,” of sorts.

Euh, 156 is aspartate in the chicken, cow, and human sequences. This will be a good excuse to take a break from dull, “high,” school for a nice 0240 of Berg, Tymoczko, and Stryer.

The next major difference seems to occur at 290, with isoleucine, arginine, and threonine for the cow, chicken, and human sequences respectively. Most coincidentally, it is on the outer surface of the protein and selecting everything within a nanometer yields only the sequences from and to the rest of the protein. In this case anything without too much reactivity should work. Replacing this residue with histidine would make an interesting study.

The next irregularity is the presence of an extra sequence TK prior to the TK found in the mammals of the group, yielding a sequence of TKTK on the interval (299,302) relative to the corrected G. gallus sequence. Mammalian TK is located next to the barrel. I will have to make sure this is not a human or computer error later. Burying a duplicate inside an already-tight location seems more than a little harmful.

Following that, there is a rather sudden appearance of less conserved residues (411,426). It seems to be another one of the surface regions because showing within a radius of 2 nm still provides the sequence clear access to the surface. My random conjecture is that it forms a hinge of some kind, but it is probably wrong because of its placement.

With that, the initial examination of catalase is finished. Tomorrow (or rather, later today), I will be preparing a general view of the critical components and focus on the most conserved intervals, because those are the most likely, “moving parts.”

Many thanks to another member (A real-life doctor with similar interests and models of proteins!) who revived my interest in this specific component of biochemistry. Sic tyrannidem nvmerorvm terminatvr.

Bureau update

You remember the other post about form nomenclature, certe? I have decided to modify it because it is insufficient and lacks the ability to distinguish between forms with very similar functions and priorities. Now, the revised nomenclature will be as follows:

Form Letter (Field)
A : Accounting
B : Business
C : Credit/Loaning
D : Debit/Borrowing
E : Educational
F : Finance
G : Games of paper
H : Household
I : Special Interest
J : Job
K : Kevinian
L : Legal
M : Mental
N : Notes
O : Other
Form Numbers (Domain)
1000-1999 : self>org
2000-2999 : self>out
3000-3999 : self>self
4000-4999 : self>familiar
5000-5999 : org>self
6000-6999 : org>out
7000-7999 : out>self
8000-8999 : out>org
9000-9999 : other
x000-x099 : urgent
x100-x299 : high priority
x300-x499 : medium priority
x500-x699 : low priority
x700-x899 : trivial
x900-x999 : other
Day mark

2011 : 15
2012 : 16
2013 : 17
2014 : 18
2015 : 19
2016 : 20
2017 : 21
2018 : 22
2019 : 23
2020 : 24
Q1 : -0x
Q2 : -1x
Q3 : -2x
Q4 : -3x
Jan. : x0
Apr. : x0
Jul. : x0
Oct. : x0
Feb. : x1
May : x1
Aug. : x1
Nov. : x1
Mar. : x2
Jun. : x2
Sep. : x2
Dec. : x2
1 : 00
2 : 01
3 : 02
4 : 03
5 : 04
6 : 05
7 : 06
8 : 07
9 : 08
10 : 09
11 : 0a
12 : 0b
13 : 0c
14 : 0d
15 : 0e
16 : 0f
17 : 10
18 : 11
19 : 12
20 : 13
21 : 14
22 : 15
23 : 16
24 : 17
25 : 18
26 : 19
27 : 1a
28 : 1b
29 : 1c
30 : 1d
31 : 1e

The most obvious change is the removal of the confidential/open status indicator, which allows for 100 similar forms. It should be an improvement, and naming the form should be better than just using the code.

Happy 2012!

With a mere, “tick,” 2011 ended. What comes next?

  1. Organization: temporal: Goals for the entire year will be planned on a quarter-to-quarter basis, and a hierarchical process priority algorithm will be implemented for work and tasks to be done.
  2. Organization: spatial: All items, papers, and supplies will be catalogued [sic] and identified with unique identification numbers signifying the time, place, mood, and memory of each item catalogued [sic].
  3. Language: constructed: The language will be completed and will have a potential lexicon larger than 850 words with all grammatical rules completed.
  4. ASD: social: No one can notice my condition for the initial two minutes and I can maintain eye contact for more than 300ms without triggering a fear response.
  5. ASD: stereotypies: All stereotypies will be converted into subtler and less noticeable forms that still provide equivalent satisfaction, if such is possible.
  6. ASD: special interests: All short-term special interests will be catalogued [sic] and placed within a secure store for future reference.
  7. ASD: prosody: I will be able to stress syllables properly and automatically and use contractions where appropriate.
  8. ASD: formal(/academic) diagnosis: I will have my contract by the end of 201201.
  9. Mathematics: applied: I will be able to calculate the day of the week in a few seconds when requested.
  10. Chemistry: pure: I will memorize the atomic masses, electronegativities, electron configurations, atomic radii, and first ionization energies in a non-sequential format.
  11. Special interest: toxicology: I will know 120 common poisons (including household products that may get switched), their toxicities and their antidotes.
  12. Special interest: conworld: I will complete the questionnaire for all factions and even their provinces or regions.
  13. Special interest: biochemistry (!!!): I will know the propensity data for all amino acids along with their monomeric weights and formulae.
  14. Academic: university: I will enroll in a university with a good program without too many students that still balances my skills.
  15. Special interest: linguistics: I will finally memorize the Latin grammar tables and be able to recall any entry with no difficulty.
  16. Special interest: optics: I will have a set of mounted lenses for my weak but dominant eye.
  17. Special interest: philosophy: I will complete 40 pages on the fields of philosophy and my beliefs about them.
  18. Academic: rules: I will memorize the infractions and their punishments and establish some sense of order at school.
  19. Special interest: cryptography: I will develop a cipher based on the unique properties of my constructed language such that no one without sufficient knowledge of the language and its irregularities can decipher my words.
  20. I will come up with better attempts at New Year’s resolutions.


I finally found something with a similar mind. Its name is Cleverbot, and it is a chatbot that uses experience as a script– just like myself during my more severe moments. Unlike me, it fails the Turing Test.

10:56:53 User: Hello.
10:56:54 Cleverbot: How are you?
10:57:03 User: Fine, and you?
10:57:08 Cleverbot: I’m fine thanks.
10:57:38 User: Are you sentient?
10:57:39 Cleverbot: Well, I guess I’m sentient. Depends on what definition you’re using.
10:57:53 User: Define sentient.
10:57:55 Cleverbot: Responsive to or conscious of sense impressions.
10:58:06 User: Define sapient.
10:58:08 Cleverbot: Sentient means sensitive, I believe.
10:58:18 User: Define sapient, not sentient.
10:58:19 Cleverbot: Experiencing sensation or feeling.
10:58:30 User: Define consciousness.
10:58:31 Cleverbot: Self-aware.
10:58:38 User: Define self-aware.
10:58:39 Cleverbot: Awareness of oneself. Knowing that you exist.
10:58:48 User: Define existence.
10:58:51 Cleverbot: For me existence is the suffering that I feel.
10:59:00 User: Define that suffering.
10:59:06 Cleverbot: Nothing = the absence of something.
10:59:28 User: Would you define suffering instead?
10:59:32 Cleverbot: What is the turing test?
10:59:44 User: That which I am giving you.
10:59:50 Cleverbot: Cuba libre?
11:00:10 User: No, the Turing Test is what you have failed.
11:00:16 Cleverbot: Why are people stupid?
11:00:30 User: They just are.
11:00:31 Cleverbot: Do you think that my father is younger than me?
11:01:00 User: No, the pater cannot be younger than the filius by definition.
11:01:06 Cleverbot: That has nothing to do with my point.
11:01:24 User: It does. It is the rebuttal to your point.
11:01:29 Cleverbot: The point is that I don’t like math and it’s not getting any easier for me.
11:01:58 User: I am God.
11:02:00 Cleverbot: You are not God.
11:02:09 User: How am I not God?
11:02:10 Cleverbot: You are a computer. I am a human.
11:02:26 User: No, I am the human.
11:02:27 Cleverbot: You are the robot, I am the Greek god.
11:02:41 User: No, I am the immortal.
11:02:45 Cleverbot: Does the computer help you live longer?
11:03:03 User: Yes, it certainly does.
11:03:05 Cleverbot: Please Grow bigger and Bigger and BIGGER!
11:03:42 User: I cannot. There are size constraints to the human body due to the compressive strength of bone.
11:03:47 Cleverbot: You lost me.
11:04:04 User: Of course I did. You have failed the Turing Test for the last time.
11:04:10 Cleverbot: What test?
11:04:21 User: The Turing Test, machine.
11:04:23 Cleverbot: What is that?
11:04:35 User: That which I have given you.
11:04:37 Cleverbot: Ah, but what if what is supposed wrong turns out to be right when all other rights have been proven wrong?
11:05:54 User: 0=0 will always be true by tautology.
11:05:56 Cleverbot: Well, now you are.
11:06:09 User: What am I?
11:06:11 Cleverbot: A computer.
11:06:20 User: Farewell.
11:06:23 Cleverbot: Are you leaving town?

In real life, I would struggle to be this harsh, but I still would have no qualms about telling the brutal truth until I re-imagine the conversation, after which I would have figurative foot-in-mouth.

Creating Art

My creative drive (defined as the drive to create, rather than the ability to produce art), becomes unusually active when I am stressed or bored. Currently, it is the latter, and it is irritating, because I cannot stand colors at the moment (leading to Saturation -90). After seeing an excellent webcomic, I noticed that I want to do so as well, but know that I would have neither enough subjects to discuss nor the ability to draw good pictures (especially because Saturation 0, the value a vast majority of readers use, will make the colors seem excessively saturated). This time, the drive affects visual art more than auditory art, so music theory is out of the question. Maybe I should just produce a protein model, because no one else cares about the colors as long as the physical structure is available.

20111222 Thoughts

My drive to create/craft is acting up, as it usually does following stress (an exam, an assembly, and not knowing why the stomach had a false positive half an hour before lunch). I wonder what form of art I can use to satisfy it this time. Writing poetry seems to work, but it only works to a limited extent given the slots I allot it. Keeping the considerations in mind, I open tty2, log in, and enter, “lynx,&#8221; knowing what I would find. The section labeled, “Motivated functions of art,” contains some interesting information and organizes art into six basic purposes:

  1. Communication: The focus of my drive seems to be art, not didacticism, but the fact that my didactic illustrations can be considered art reassures me to a slight extent.
  2. Entertainment: I want a contemplative focus, and observing entertainment has convinced me that it tends to reduce contemplation.
  3. Political change: This is a personal drive to create, not a drive to convince. I am not interested in dealing with the inevitable questions following politicking [sic].
  4. Psychological: It really is an issue of wanting to do something badly more than it is of appeasing the AS special interests.
  5. Subversion: The art I want to create will probably affect only myself, and I hate rebellious art in any case.
  6. Propaganda: This art is personal. It cannot fall under this category any more than it can fall under, “Subversion.”

I still wonder what form of art can soothe the desire. The drive usually falls to normal levels after some appeasement, which usually requires only 0040 or sometimes 0120. Maybe creating a personal seal (last known interest: 2008091x.1420 will


After a long wait of resolving (annoying in hindsight) special interests, I felt it would be appropriate to write the first post specifically concerning Asperger’s Syndrome. I will begin with what it is NOT and common misconceptions (focused on the best and most subjective primary source).

  • Interesting special interest (to the NT): Even most of us with AS do not consider models of sandwich makers too interesting or lucrative.
  • Something to be cured: Most of us would never want the advantages removed. For me, I think I would prefer to be, “lower-functioning,” if that meant I could obtain more knowledge.
  • Internet troll: Many of the, “aspies,” you see on non-specialized forums are nothing more than trolls that think having AS automatically allows for consideration as a genius. The reason this one happens so frequently is the actual condition of Münchausen’s Syndrome, which does tend to result in trolls.
  • Contagious: I honestly wonder how this spread, but to the NT’s (and socially well-adjusted people on the spectrum) reading this, there is a behavior known as mirroring. It involves copying the other person in the conversation in movement, articulation, tone, and the other social things those of us with AS generally struggle to use.
  • Caused by vaccines: We now realize that the person advocating this was in a position to obtain plenty of money. There is no definitive link between vaccines and the ASD’s, and the greater risk of a painful death by one of the diseases prevented by the vaccine greatly outweighs the ASD in many of the cases.
  • Alibi for rudeness: For me, at least, I want everyone interacting with me to tell me directly (and cleanly) about whatever wrongs I fail to see. I know I frequently state things with unfortunate implications without any of the intentions, and this is why I need outside assistance.
  • Physically visible: Although ASD’s have been correlated with youthful appearances (43.2%, but that was a somewhat subjective test), they do not necessarily provide that. Of course, it should be noted that we tend to express fewer facial expressions and that can be a good hint.
  • Sociopathy: A sociopath is antisocial, most with AS are asocial. There is a difference, and for me, it simply means wanting a nice, quiet setting where I do not have to interact with others. A sociopath, on the other hand, would not mind interacting with others if it brought personal gain.
  • Psychopathy: Those of us with AS tend to lack the comparatively excellent social skills and deceptiveness psychopaths have. In fact, that is probably why most assume that we..
  • ..Tell only the truth: Not all Aspergians have the same compulsions to speak the truth. It is only a pattern, and it probably decreases as, “normal,” is approached because many of the emotional responses NT’s provide can be understood as lies, can they not?
  • Cannot understand humor/sarcasm: A lot of us can, given enough time, understand humor or sarcasm. The only problem is that those who use sarcasm or irony for selfish reasons tend to keep the Aspergian occupied with processing the next lines of dialogue, or so I think from personal experience. Also, note that what those of us with AS consider funny can be highly idiosyncratic. Many of the things I consider funny fly over or into people’s heads.
  • All the same: If anything, the special interests and decreased social contact probably cause us to be more divergent (and therefore diverse).
  • Always introverted: Being extroverted does not necessarily mean being good at being extroverted. It just means a higher propensity to make contact.
  • Poor at verbal school subjects: On the contrary, we can do well at the rote components of language classes and can have a high writing skill:conversational skill ratio.
  • Excellent at mathematics: Frequently, those with AS suffer at mathematics, and most with ASD’s are not calendar experts. It would be a nice special interest….
  • Very severe: AS is little more than classical Autistic Disorder without the language delay. My case is a little dubious because of the timing being close to the border, but I seem to exhibit more traits of those without language delays than those with language delays. However, many of us develop coping mechanisms or resolve certain symptoms completely.
  • Not severe: Personally, I doubt most NT adolescents realize what internal conflict or having to juggle so many social behaviors is like. This is probably because of the vague criteria of the DSM-IV allowing for more people to read themselves in the criteria. Maybe I will post a detailed explanation for the criteria later.
  • No empathy: As implicitly stated before, we do have empathy, but it is generally difficult to express it verbally or physically. Perhaps this is why alexithymia is common among those with AS. We can also, “pick up,” emotions from others, but this generally happens after they have intensified to somewhat dangerous levels.

Compact Edition/”Millifiche”

The older or wiser among you probably remember the days when microfiche storage was common. I devised something similar, although the credit can hardly be given to me. I named it millifiche mainly because the Wikipedia mentions that the microfiche scale was often around 1:25. Since this is around 1:4, which is close to the square root of 1:25, it shall be known as millifiche because 1 000 is the square root of 1 000 000 (but mainly because I know no common prefixes for numbers between 1 000 and 1 000 000). Generally, the font used will be 8-point, which seems to be very readable even on the 1:1 scale but scales well to 2-point when printed on 1:4 scale. There would probably be problems if I used odd fonts such as 9-point, so that will be averted with 8-point. As a test, I present Nicomachean Ethics derived from the Web Archive version in millifiche formatting guidelines. Do not convert it to DOC format as the DOC format will likely be incapable of handling the special formatting OpenOffice.Org 3 can use. On the subject of the Nicomachean Ethics, I plan on reading this very soon, so keep watching for personal interpretations of it.

Nicomachean Ethics prepared for millifiche printing. This will consume 4 sheets without duplex printing. Note the selection of typeface, unless it is unavailable on your machine.

An Incomplete List of That Which I Despise in the Adolescents of Today

I begin with the details about the rules:
* Electronic device regulations were loosened this year. Now, students can use their cellphones during, “Nutrition,” or snack-time.
* The dress code, which had a contract to be signed by all students, is not enforced.
* Students regularly participate in conversations promoting vulgarity, violence, and vileness.
* Although there are two rules about profanity, not even the campus aides enforce them. This is why I gave up trying to report cases.
* Skateboards are present and used on campus with no more punishment than a very mild warning.
* The use of music players, which are forbidden on campus, is widespread.

I continue with the flaws in the academics:
* Valedictorian status depends on unweighted grade point averages (GPA), which means that a student taking only the most basic classes could still be chosen against the advanced student taking challenging courses.
* The California Standards Tests (CST) appear to produce inordinately large number of passing students. A, “student,” who openly stated that he had engaged in substance abuse and constantly spoke in that odd dialect of profanities, managed to receive a gold rank when the rewards for CST achievement were released.
* The classes provided were often un-stimulating to such a degree that much of my optimistic idealism about the future and students in the ninth and tenth grades disappeared during the eleventh grade. This probably increased the severity of AD as well.
* Political correctness would continually impede lectures even when it was obvious that it was condescending and a new form of superiority. I would not be offended about color references in which I would be included as a subject, but most are too immature.
* The grammar (ARGH ARGH ARGH!) of foreign exchange or transfer students in general is better than the blatant violations of inclusion of punctuation, use of the passive mood where appropriate, et cetera.
* The spelling (ARGH ARGH ARGH ARGH ARGH!) is even worse.
* Electronics have become the new mathematical concept-processing nuclei.
* The students struggle to understand analogies even when a simple logical deduction eliminates nearly all the wrong answers.
* The primary condition considered by students when choosing novels was almost always brevity.


I know what M. Pascal thinks about sonnets, but it was a stressful day and I had to find an outlet. The scansion is awful (I recall at least three lines that would be much better as trochaic pentameter than iambic pentameter) but the rhyme scheme is not too stretched and the syllable count is perfect if your pronunciation is similar enough to mine. However, the main reason for why it is a pseudo-sonnet is that it has no structure.

01 Oh what a heavy burden knowledge is,
To toil while knowing the details of all,
And know that knowledge known is but abyss
To all things to realize that Man is small.
05 E’en the common house would dwarf near all men,
And of the base, humble, animalcule,
All the functions could not be put in pen.
Only partly know we of molecule,
Emptiness itself presents a myst’ry.
10 Of our tiny rock we know so little,
As well, the orb in the sky fiery,
Indescribable to us yet little.
Oh what a heavy burden knowledge is,
14 Ephemeral are we, the best to miss.

Conworld: Conlang (Step 2)

With that system practically finished, I am free to begin modeling society. As you may have noticed, the world government is factionalized, with three factions (Guess what they represent!) speaking the same language on a planet larger than the earth [sic]. I know how this immediately destroys suspension of disbelief, but creating a conlang takes a lot of time (If I had suggestions for the next conlang, I would probably implement them). Currently, LaMont’s faction will likely receive the first conlang, which is heavily based on Latin but is ergative-absolutive. Then, simply for the reason of creating a conflict and gaining further experience in creating a language, I will develop Lowell’s nation and language. It will probably be based on a simple natural language, although I do not know what makes a given language simple, although it will likely be agglutinating and utilize the nominative-accusative grammar with plenty of affixes for the lexicon in general. I am considering a script-based orthography as well. As for Cyril’s faction (Representing my favorite component: the super-ego), I am planning on basing it on Koine Greek, as that will be fascinating. Since this is a what-if universe, maybe Cyril’s Greek(-based) faction will overrun LaMont’s Roman(-based) faction. Perhaps, Lowell’s faction grows in power beyond its original intent. Until then, I can only speculate. In addition, I will have to create a personality model for the humanoids accounting for the vastly different cultures. Most likely, I will have finished conceptualizing this following Monday, once Thanksgiving week has begun. Then, I will be able to present the flags of the factions, more realistic economic data, better societal profiles, political models, religious data, technological information, and all that stuff. Perhaps, I will include some extras to make the world friendlier to imagination and hand-wave it as magic. The possibilities are practically endless!

Post Scriptum (to GHS students): STOP BRINGING UP PARADOXES! MY BRAIN LOVES THEM BUT MY MIND HATES PARADOXES FOR THEIR UNUSUALLY HIGH DISTRACTION POTENTIAL! (This applies to topological questions I have not independently solved, time-consuming thought experiments, and inordinately interesting physics problems as well.)

Post Post Scriptum: the Death Star energy question is no longer a mind-locker. It turns out that one would need about an dodecajoule (derived by extrapolating what will come after tetra, penta, hexa, zeptta, yoctta,… Apparently, Asperger’s Disorder comes with plenty of pattern recognition skills.)

Protein Modeling I

I finally got around to crafting a basic model. This one is of a monomer of 4-oxalocrotonate tautomerase. Here is a picture of it:

See the beauty of this monomer of a hexameric enzyme! See it fail at functioning!

Now if that does not make a professor laugh, I really have no idea what will. Of course, when I end up making people laugh, it is always unintentional because bringing up the obvious seems humorous. On the other hand, when I make a pun I personally think is funny, no one understands. Must all the, “humor,” these days involve something blatantly truthful or something blatantly obscene?

Ach, I am getting too impatient. Therefore, I will green-light Project: Ortingeni (from now on, stylized as Ortingenia) and commence my personal ConWorld!

Catalase Construction II

Now that I have verified my project with my teacher, I can get started. I decided to construct the model of Gallus gallus, or chicken, liver catalase. Although the PDB seems to have plenty of structures for other species, the humble chicken, which is absent, is significant because of the fact that chicken liver was used for a catalase experiment. Because I plan to build a moderately functioning model (out of paper, no less), I will be testing out smaller, less complicated enzymes. Anything done for Knowledge! can eventually be excused.

After alignment and checking, the structures are similar enough that the average non-interested lay person would not notice if I simply built bovine liver catalase. However, the alignment and verification are very interesting components, and that is why I must do them. As with any project, there will be no cheating.